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How to Diagnose Sinus Headache vs Migraine

Author Iman Iqbal covers How to Diagnose Sinus Headache vs Migraine on BackTable ENT

Iman Iqbal • Updated Sep 27, 2025 • 35 hits

Headaches are among the most common reasons patients seek ENT care, and many assume that sinus problems are to blame. Pressure, congestion, and facial pain are often labeled as “sinus headaches,” yet studies show that many of these cases are actually migraines or other non-sinus conditions in disguise.

This article explores the challenges of distinguishing true sinus disease from look-alike conditions, why misdiagnosis is so common, and how careful evaluation combined with modern, integrative approaches can improve outcomes.

This article features excerpts from the BackTable ENT Podcast with otolaryngologist, Dr. Jessica Lee. We’ve provided the highlight reel in this article, and you can listen to the full podcast below.

The BackTable ENT Brief

• Headaches commonly attributed to sinus disease are frequently found to be migraines or other non-sinus-related conditions.

• Symptom descriptions such as “congestion” are often vague and misleading, since they may refer to airflow restriction, facial pressure, or even cognitive symptoms like brain fog.

• The overlap between allergic symptoms and migraines complicates the diagnostic process and may lead to confusion.

• Misdiagnosis is common, with research indicating that up to half of patients treated for sinus infections demonstrate normal findings on CT scans and nasal endoscopy.

• Comprehensive diagnostic evaluation increasingly includes symptoms beyond nasal complaints, such as dizziness, nausea, ear fullness, and sensitivity to light or sound.

• Objective tools like imaging and real-time nasal endoscopy provide crucial evidence to clarify whether symptoms are due to sinus inflammation or alternative causes.

• Lifestyle factors, including poor sleep, chronic stress, dietary triggers, and prolonged screen exposure, are significant contributors to migraine-like symptoms that can resemble sinus disease.

• A holistic, patient-centered approach that addresses daily habits and potential triggers often yields more effective and sustainable relief than reliance on medications or surgical intervention.

How to Diagnose Sinus Headache vs Migraine

Table of Contents

(1) Headaches: Allergies, Migraines or Sinus?

(2) Evaluating Sinus Headache: The Importance of a Precise History

(3) Headache Triggers: Nutrition, Sleep & Stress

Headaches: Allergies, Migraines or Sinus?

Sinus headache is one of the most common complaints ENT specialists hear, but it is also one of the most frequently misunderstood. Many patients describe pressure, pain, or congestion, and attribute these symptoms to sinus issues, even when the location of discomfort doesn’t align with sinus anatomy. The challenge lies in vague terms like congestion are, which can mean anything from airflow restriction to heaviness or fogginess –making detailed interview essential. Clinicians must distinguish between sinus-related pathology (rhinogenic headache) and other causes like migraines or tension headaches (non-rhinogenic).

The complexity deepens when patients present with overlapping conditions, such as allergies that mimic or worsen headache symptoms. Providers are then left to determine which issue is truly driving the discomfort. Mislabeling migraine as sinus disease is common, often leading to years of unnecessary interventions – from antibiotics and immunotherapy to sinus surgery – without lasting relief. Dr. Jessica Lee discusses studies that show that up to half of patients diagnosed with sinus infections have normal CT scans and endoscopies, underscoring the high rate of misdiagnosis. This highlights the importance of precise questioning, careful evaluation, and collaboration across specialties, since “sinus headache” often masks a more nuanced interplay between migraines, allergies, and true sinus pathology.

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[Dr. Ashley Agan]
Diving into the topic of sinus headache. Let's just set the stage because I think we all, as ENTs, this is such a common thing that comes in, whether people are describing it as sinus headache or just sinus. Some people just have-

[Dr. Jessica Lee]
No pressure.

[Dr. Ashley Agan]
-sinus or they're pointing. What is that, and how do you think about it?

[Dr. Jessica Lee]
I think that's an important point to start with, that this is what patients tell us, right? They come in and they say, "I have sinus headache or I have sinus or sinus issues." When you start to question them further, a lot of times it is going to include some type of symptom of pain or pressure in the face, typically, but I have had people tell me I have sinus issues, and they'll point to their temple or the back of their neck. I can sometimes gently say, "Well, there really aren't sinuses there." Anyway, point being, it's some type of facial or head pain or pressure.

Usually, they're going to also use the word congestion, which I find to be one of the least helpful words in our vocabulary because it means so many different things for so many different people. Again, I usually end up questioning further, "Is that airflow problems in your nose when you breathe in? Is it airflow problems when you breathe out? Is it pressure? Is it heaviness? Is it fogginess?" You have to dig through what that actually means because it's different. Essentially, I like to talk to patients about sinus headaches because what I began to notice is how often that symptom is misdiagnosed as a sinus infection.

We have to be very careful, I think, in our field because people are going to come to us for this. If we're not, honestly, the experts at teasing this out, then that misdiagnosis cycle is going to continue. If you really want to be technical about the terms, there's rhinogenic headache, which is a headache that we attribute to a true acute sinusitis or a chronic sinusitis or sinusitis with polyps. Then there's non-rhinogenic headache, which is really more in that primary headache bucket, which includes things like tension headache and migraine disorder and things like that. That's where that it all starts.

[Dr. Gopi Shah]
The sinus headache, is it its own entity, or are we just talking about a symptom of sinusitis?

[Dr. Jessica Lee]
I actually think it's a symptom, correct. Actually, there is not an ICD-10 code for sinus headache, right? That's the other confusing part is when you're starting to try to think, "Well, how can we study this?" You're going to have to use the migraine codes, the atypical facial pain, tension headache. Honestly, the term sinus headache, they group it under-- I think it's one of the J32 codes of chronic sinusitis, but in actual fact, there's a review that says 80% of sinus headache complaints actually meet criteria for migraine disorder.

I don't think it's, "Well, we don't have a great code for it. We don't have a good way to talk about it. We don't have a way to code for it." It makes it, I think, hard for us to start teasing it apart completely, I don't know, at the big level, right?

[Dr. Ashley Agan]
Yes. I would say, when I have patients that come in specifically with that as the main, that's the chief thing that's bothering them, it is more likely for the exam to be unimpressive. If I actually see polyps or pus or some sort of sinus pathology, I'm surprised and like, "Oh, yes. You do have a sinus infection or whatnot." I would say, most commonly, there is not an obvious sinus pathology. I think as ENTs, we are trained really well to treat sinus pathology. If we see polyps, if we see pus, I think we're really good at that. I think these patients can be really tricky because a lot of times, they might have an exam that is not super remarkable. I don't know. What is your experience?

[Dr. Jessica Lee]
Again, I like to use real-world data. Again, there was a review, and it said that 50% of patients diagnosed with sinus infection actually have completely normal endoscopy and CT scans. It's a problem of misdiagnosis mostly, but you're right. We are trained as people who know sinus pathology. What do you do when that patient walks in and they're telling you, and they're usually going to say, "I've got sinus headaches. I've got congestion. Yes, maybe I have a little post-nasal drip." Then you're ticking off those criteria for ARS and CRS and you're thinking, "Well, it could be." Then you do their CT or you do their endoscopy, and it's nothing.

The question is, what do you do next? I think there's a tendency, maybe, with some of the training that, "We're done. We're out. It's not us. It's a headache issue." The problem is there's only, I think, 700 headache specialists in the US versus there's 10,000 ENTs. Again, when patients start saying the word sinus, congestion, headache, whatever they want to add to the word after it, they're going to be referred to us. I think there's a gap in our training, but also in our comfort level and working with these patients. I think that can change.

[Dr. Gopi Shah]
Do a lot of these patients, I feel like they also have allergies, too. How often is it not a sinus issue, but it's a symptom of allergies? Because I see a lot of that as well, where it's boggy turbinate, clear rhinorrhea, and then the pressure. It's not quite sinusitis, but they have the headache, and it's that allergy season. Is it different?

[Dr. Jessica Lee]
No, I think it can be both. That's the other hard part, is you can have patients who are having headache symptoms, and you happen to allergy test them or scan them, and they come back positive. Then again, what do you do? What do you treat first? I think most ENTs would agree, we're going to go with what's abnormal, right? You're going to treat their allergies or you're going to treat their sinusitis, but then what if they still have headaches? One of the most clear examples of this I had a few years ago was a young woman. She was about 31 years old.

She had been years of symptomatic or she had symptoms for years, and she had been through allergy testing and immunotherapy, completed her five years, and didn't really get that much better. Then she had sinus surgery, although we'll talk about her CT being normal, actually, but she did have sinus surgery, didn't really change her symptoms. Finally, by the time she came to me, she said, "The place I go has recommended I do allergy immunotherapy a second time. I was like, "Hang on, let's just pause for a minute." We went through and we dissected it out. For her, it was absolutely migraine.

She just continued to go to urgent care or primary care and be prescribed antibiotics and steroids, and things would get better temporarily, because migraines do get better. Really, it can be difficult because you have patients that have not just one problem. Our bodies don't read the textbooks, and so it's not always clear-cut, so you have to detect a bit.

Listen to the Full Podcast

Sinus Headaches vs. Migraines: Diagnosis & Treatment  with Dr. Jessica Lee on the BackTable ENT Podcast
Ep 228 Sinus Headaches vs. Migraines: Diagnosis & Treatment with Dr. Jessica Lee
00:00 / 01:04

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Evaluating Sinus Headache: The Importance of a Precise History

Diagnosing sinus headaches remains a challenge because so many symptoms overlap with other conditions. Patients often report relief from treatments like prednisone or antibiotics, but these medications have anti-inflammatory properties that temporarily ease symptoms without addressing the true cause. Traditional history-taking still focuses on pain location, congestion, drainage, and smell loss, but more ENT-focused approaches include questions about dizziness, ear fullness, tinnitus, nausea, sensitivity to light or sound, and whether weather or hormonal changes trigger symptoms. These additional details can help distinguish between sinus-related pathology and conditions such as migraine or vestibular migraine, which frequently masquerade as sinus disease.

One of the biggest hurdles is convincing patients that their recurring sinus headaches may not be sinus infections at all. To address this, clinicians emphasize examining patients during active episodes and sometimes order CT scans to show whether the sinuses are truly inflamed. Clear imaging and direct feedback often help patients understand the diagnosis. While most cases turn out to be migraine, careful evaluation remains essential to rule out other causes, from tension headaches to more serious conditions such as cluster headaches or vision-related disorders.

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[Dr. Ashley Agan]
Yes, I think that whole response to treatment, I think, does muddy the water because a lot of things will respond to prednisone. It's a very powerful anti-inflammatory, so when people say, "Oh, yes. I felt better for a little while." Even antibiotics can have anti-inflammatory effects, and so that can certainly make it confusing. Obviously, patients are coming in, and you mentioned a lot of the symptoms that they will present with. When you're taking your history, what are some things that you've started asking about that maybe you didn't ask 10 years ago that help with figuring out the etiology of this?

[Dr. Jessica Lee]
Yes, that's a great point because, like you said, you're going to get from your medical assistant or whoever's helping with your HPI, you're going to get the information typically about where the pressure and pain is, what it feels like. You're going to get the nasal symptoms, whether it's airflow obstruction or mucus or purulent drainage, and the loss of sense of smell, which is those four core components we always think to ask about, but I've started asking more about dizziness. Are they having dizziness when they're symptomatic? Do they have ear fullness? They'll often say, "Oh, yes. I go to urgent care, and I get diagnosed with an ear infection and a sinus infection, and I get put on my antibiotics."

I'm like, "Okay, we're going to double-check that. I ask about nausea and vomiting. I ask about sensory phobia. I say, "When you feel like this, do you feel like sounds are louder or more uncomfortable, or do you feel like you don't want to be around bright light as much, or smells, can you not tolerate certain smells?" I ask them about tinnitus. Do they have tinnitus during that time? Do weather changes stimulate it? That's back to, Gopi, what you asked about with allergies, is a lot of people assume, "Oh, will the weather change?"

[Dr. Gopi Shah]
I know when the weather's changing, because I'm that patient. I get the headaches, and sure enough, six hours later, there's clouds or something brewing. I'm like, "Okay."

[Dr. Jessica Lee]
It's that barometric pressure change, which we know is part of migraine pathology, and it can be part of allergy pathology, but which one is it? Hormones, for women especially, asking about, does this have any relationship to their menstrual cycle? That's a big clue. That's the list of things I've added to the HPI questions.

[Dr. Gopi Shah]
With those questions, I think of nausea, vomiting, sensory, that's my migraine bucket. I think of ear fullness, congestion with my sinus bucket. With dizziness, could it be vestibular migraine? My guess, if it has some sinus component, maybe that's still my sinus bucket. Tell me, how do you use some-- Do you get nausea, vomiting with your sinus headache, or is that no?

[Dr. Jessica Lee]
Yes. I think that's probably one that people don't get as much. Maybe a little nausea, maybe a little queasy, or maybe they just don't have an appetite, but they're typically not coming in saying, "I have a headache and I vomit and I'm sensitive to light," because if they say that, they go to neurology for migraine. It's more subtle. I think, for me, the ear fullness, the dizziness, the tinnitus questions bring in the vestibular migraine potential, which again is still a migraine diagnosis. Then, like I said, I think the sinusitis piece of it is what generally happens is if this is someone who's having recurrent acute episodes, what I will tell them, because by the time they come in, they're not in an episode anymore.

Very likely, their endoscopy does look normal. What I will tell them when they come in is, "The next time you get sick, I want to be the one to see you. I don't want you to go to urgent care. I don't want you to even go to your primary care. They do a great job, but I do this, and I want you to come see me." I'm lucky that I work in a practice where we are very accessible the way the practice is set up. I'll also give them my work email, and be like, "Look, if you call and you can't make it in, just email me and I will book you, because I want to see you when you are symptomatic. I want to see, is there pus dripping out of a sinus? Is there really fluid behind your eardrum."

In some cases, I'll even go as far as to say, "Next time you come in and you feel this symptom, I'm going to do a CT scan and we're going to see what it shows." I find that feedback for patients is extremely helpful, because unfortunately, you bring up the word migraine, there's a stigma. People shut down. They don't want to be diagnosed with migraine. A lot of people, it's hard to convince them that these sinus headache episodes are actually not infections. Sometimes, having that feedback where I can go over their CT scan with them is extremely helpful.

[Dr. Ashley Agan]
I'm so glad that you also have a hard time convincing people that it's migraine, because I have the same experience where we have good data to back up. Can you tell patients, "Actually, a lot of sinus headaches are migraine. Look, your sinuses are clear." You're right. People don't want to have migraine, or they're like, "No, I'm not a migraine patient. That's not me." I'm glad to hear that even you have this issue. In thinking about your differential, these sinus headache patients, where it's, what did you call it? Non-rhinogenic?

[Dr. Jessica Lee]
Yes. Non-rhinogenic headache, yes.

[Dr. Ashley Agan]
Right. There's not an acute sinusitis. Is the most common diagnosis migraine? Are there other things on your differential that you're thinking about?

[Dr. Jessica Lee]
Yes. Certainly, you have your warning signs. If you have someone who has new-onset headaches, especially if they're older. If they're having any other systemic symptoms, if they're having vision changes, you don't want to forget that headache differential and just automatically assume it's migraine. Again, I would say the vast majority of the time, that's not really on the radar. I would say, I think I did have a patient a couple weeks ago who was having vision changes with new-onset and progressively worsening headaches. I was like, "Okay. You were going to get an MRI because we need to take a closer look before we just label this."

I think the differential is still, if someone comes in, their primary complaint is sinus headache, I still think your differential will include acute sinusitis, chronic rhinosinusitis, migraine, tension headache. Then you've got some other things. You've got the more rare or less common things like cluster headache and things like that. Again, I'm not a neurologist. I'm not claiming to be a headache specialist, but I think that these types of headaches present in our clinics much more commonly than in other specialty clinics. Again, I think it's a place where we don't get the training, and I think that it's a place where we can do better for our patients.

Headache Triggers: Nutrition, Sleep & Stress

When patients present with sinus-like symptoms but have a normal nasal endoscopy, the underlying issue is often migraine rather than sinus infection. These patients may experience congestion, runny nose, or facial pain due to nerve hypersensitivity in the trigeminal system, which can mimic sinus disease. Instead of immediately labeling it as “migraine,” providers sometimes explain it as a nerve sensitivity linked to overall brain health, emphasizing the role of lifestyle factors such as sleep, nutrition, stress, and hormones. Exploring these aspects during a visit often reveals patterns that help explain recurring symptoms.

One of Dr. Jessica Lee’s cases highlights how lifestyle adjustments can be more effective than repeated antibiotics. A young man with frequent “sinus infections” was actually experiencing migraines worsened by long fasting periods, poor nutrition timing, and extended screen exposure. By encouraging regular meals and visual breaks, his symptoms improved significantly. While tools like continuous glucose monitors (CGMs) can provide deeper insight into blood sugar patterns and migraine triggers, most patients gain clarity through simple conversations about eating schedules and daily habits. This practical, integrative approach often helps patients connect their routines with their symptoms, leading to meaningful relief without unnecessary medications.

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[Dr. Gopi Shah]
Let's say you have that patient who is able to see you in clinic, the symptoms of headache and congestion, some ear fullness started, you see them in clinic, what do you do? What is that visit like? Tell me what sometimes you'll see in these patients and your findings.

[Dr. Jessica Lee]
Like Ashley said earlier, I think, honestly, most of the time their scope is normal if it's a migraine patient. Now, you're right. Sometimes, you're going to get the overlap. Maybe they have allergies as well, and you'll see some buggy turbinates or a little bit of clear mucus in the nasal cavities. If you see purulence, you're obviously going to treat it along the guidelines for acute or chronic sinusitis, but let's assume in this case that this is a normal endoscopy. Then, at that point, like I said, if it's recurrent acute, I'll usually say, "Okay, let's think about the possibility."

I sometimes won't even use the word migraine. I'll say, "What if this could be like a nerve hypersensitivity," which is migraine. I'll explain how the trigeminal nerve gives them sensation in their face and in their sinuses, and how you can have autonomic symptoms. You can have runny nose and congestion because of the parasympathetics in that area. I give them a little brief, like, "Hey, this is how your nerves in your face work." I say, "Let's think about what makes nerves hypersensitive, and it's anything that impacts your brain health. That's your sleep. That's your nutrition. That's your stress levels. That's your hormones, all those things."

From there, I usually will try to have a little conversation about their daily habits. I'll give you another example. This is a young man in clinic a couple of weeks ago, and he, again, had been treated for recurrent sinus infections all coming up in the past couple of years, but when he told me about where his headaches are, he kept pointing to his temple. I was like, "Okay." His scope was normal and everything. I said, "Let's just talk about some of these other things like we just listed." It turns out, for him, he fasts all day long.

I was asking about his normal routine of eating because a lot of times, too, with migraine, I'll tell people, 'It's not as much what you eat. There are certainly foods that are known to be triggers, and it can be different for everybody." A lot of it is the pattern and how long you go in between and those periods of hypoglycemia. For him, he was like, 'Oh, I rush out the door in the morning to get to my job. I sit at my desk all day long. I don't take a break for lunch. I basically eat dinner, and that's it." I was like, "Okay, we're going to think about getting you on a more stable nutrition plan."

Also talked about like that constant screen time with no break and that constant visual stimulation and taking a break every hour, get up, go walk around, go step outside for two minutes or something. He came back in and is already feeling better just from tweaking a couple of things like that.

[Dr. Gopi Shah]
When you talk about hypoglycemia, that makes me think about a CGM, a continuous glucose monitor. Are you using those in your practice at all to help patients have more insight into what might be happening, how they can track their symptoms with how their glucose is tracking? Do you have any thoughts on that?

[Dr. Jessica Lee]
I'll tell you, I've done a CGM just for curiosity's sake. It's not hard to do, and you can gain some really interesting insights. What I will say is, number one, for most people, it's going to be an out-of-pocket expense. It's not going to be covered by insurance unless they have diabetes. In my experience, you don't even need that. You can tell just by asking a few questions about what time do they normally eat breakfast? What time do they normally eat lunch? What time do they normally eat dinner?

Right away, you're going to get an idea of is this someone who-- or you'll have a patient who comes in and says, "Oh, I started intermittent fasting, and now I'm having these headaches." I haven't found that I needed to use it clinically. I do have some patients who I work really in-depth with from this integrative standpoint. We have kept it in the sides as like a, "Hey, if we feel like we're struggling and we really want to get further insight, we can use this." Honestly, none of them have needed it.

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Podcast Contributors

Dr. Jessica Lee discusses Sinus Headaches vs. Migraines: Diagnosis & Treatment  on the BackTable 228 Podcast

Dr. Jessica Lee

Dr. Jessica Lee is a practicing otolaryngologist and lifestyle medicine specialist in Charleston, South Carolina.

Dr. Ashley Agan discusses Sinus Headaches vs. Migraines: Diagnosis & Treatment  on the BackTable 228 Podcast

Dr. Ashley Agan

Dr. Ashley Agan is an otolaryngologist in Dallas, TX.

Dr. Gopi Shah discusses Sinus Headaches vs. Migraines: Diagnosis & Treatment  on the BackTable 228 Podcast

Dr. Gopi Shah

Dr. Gopi Shah is a pediatric otolaryngologist and the co-host of BackTable ENT.

Cite This Podcast

BackTable, LLC (Producer). (2025, June 24). Ep. 228 – Sinus Headaches vs. Migraines: Diagnosis & Treatment [Audio podcast]. Retrieved from https://www.backtable.com

Disclaimer: The Materials available on BackTable.com are for informational and educational purposes only and are not a substitute for the professional judgment of a healthcare professional in diagnosing and treating patients. The opinions expressed by participants of the BackTable Podcast belong solely to the participants, and do not necessarily reflect the views of BackTable.

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