Irregular periods: Is it PCOS, hypothalamic suppression, or something else?

If you’ve struggled with irregular periods, you might have noticed it can be a little tricky to figure out exactly what’s going on—and, therefore, exactly what you need to do to get your period back. 

In this episode, Lara discusses:

• the two most common explanations for irregular periods,
• how to tell them apart, and
• how hypothalamic amenorrhea is frequently misdiagnosed as PCOS. 

Links:

• Prof Jerilynn Prior's paper about hypothalamic suppression
• PCOS cannot be diagnosed by ultrasound
• Cyclic progesterone therapy for PCOS
• Lara's metabolism book

Transcript

Welcome back to the podcast. I’m your host, Lara Briden, a naturopathic doctor and author of the books Period Repair Manual, Hormone Repair Manual, and Metabolism Repair for Women.

I’m currently working on a new book about periods. So, I’m back in my happy place, which is writing, researching, and thinking about periods. And if I’m honest, it’s quite a relief to be writing about periods rather than perimenopause—the topic that has absolutely dominated in 2025. Not that perimenopause isn’t important. Of course it is. I wrote a whole book about it.

But the hormones of young women are also important. I’m talking about women in their teens, twenties, and thirties, who are supposed to be making hormones with regular ovulation, but often are not. Either because their ovulation has been switched off with hormonal birth control, or because their brain-ovary communication is just not doing what it’s supposed to be doing. If that’s your situation, this episode is for you.

Let’s start with a quick refresher: If you’re of reproductive age, then regular ovulation is how you make hormones. You make estradiol, your main ovarian estrogen, in a big spike just before ovulation, and then—if you managed to ovulate—you make progesterone for about two weeks afterwards.

It’s also entirely possible to have a cycle where you make estrogen, but did not manage to ovulate, so made no progesterone. But because there’s estrogen, you still have a bleed, sometimes a regular bleed. That’s called an anovulatory cycle, and it can appear like a normal cycle, or period, unless you actively look for a luteal phase with a blood test or temperature tracking.

Right. So, where do you start with assessing irregular periods?

Should you test estrogen and progesterone? Well, that can really only tell whether ovulation is likely to occur—or has occurred— in that cycle. And only if you sample on exactly the right days for your cycle. And that can be quite hard to do.

And actually, cycle charting with temperatures can provide similar information and, in many ways, is better than progesterone testing because it can tell you about the quality and duration of the luteal or progesterone phase—something a spot blood or urine test cannot.

Whether you test progesterone or track temperatures, finding out you’re not ovulating is really only the first tiniest step in assessment. The real question is why you’re not ovulating. So, the next and most important steps involve testing for and ruling out all the possible explanations, such as pregnancy, obviously, but also things like underactive thyroid, high prolactin, a medication side effect, such as from some antidepressants, a deficiency of iron, vitamin D or really any nutrient, or an illness like autoimmune disease, including celiac disease. Even a history of concussion can impact periods.

Now, if you can identify an underlying problem, such as an underactive thyroid, high prolactin, or celiac disease, then the way to regulate your period is to fix or address that underlying problem. That should be all you need to do.

Of course, another possible explanation for no periods, that I’ll just mention, is primary ovarian insufficiency—also called POI, which means full menopause or periods stopped before age 40. That’s one of the scarier of the possibilities, I know—and many of my patients are worried about that. But, fortunately, POI is both fairly uncommon and fairly easy to rule out with an FSH test. If your FSH is repeatedly below 25, then it’s very unlikely your lack of periods is from primary ovarian insufficiency or early menopause. Instead, something else is going on.

And just a reminder that FSH (or really any hormone test!) cannot diagnose or rule out perimenopause. Instead, perimenopause needs to be assessed based on symptoms and context. See my perimenopause book for more about that.

For today, let’s get back to the problem of irregular periods, or a lack of periods, in young women— women under 40. Once the major medical causes have been ruled out, the two most common explanations are hypothalamic amenorrhea, including milder hypothalamic suppression, and I’ll explain what that is, and PCOS or polycystic ovary syndrome. They’re quite different from each other, yet there is overlap, and potentially a lot of confusion because hypothalamic suppression is frequently misdiagnosed as PCOS.

As we start to think about these two common situations, remember the basic principle that to achieve a regular period, you need to correct or fix the underlying problem or obstacle that is preventing regular ovulation.

In the case of hypothalamic amenorrhea or suppression, the obstacle to ovulation is that your hypothalamus — which is your brain’s hormonal command centre — has decided that conditions are not right to make a baby. That’s true even if you don’t want a baby; that’s just how periods work. The poor conditions could be stress, illness, overtraining, or, most commonly, undereating. And that could be undereating generally, or undereating carbohydrates, more specifically. Although not every woman is sensitive to a low-carb diet in that way.

Milder hypothalamic suppression can show up as a shortened luteal phase or anovulatory cycles, which can actually cause heavier-than-normal bleeds because it’s a situation of enough estrogen but too little or no progesterone. More severe suppression (such as from more severe undereating) can cause long cycles, which means long gaps between bleeds, or eventually amenorrhea, which is a complete lack of periods. Estrogen would be very low in that situation of a complete lack of periods, but only with hypothalamic suppression, not with PCOS, as we’ll see.

Descriptions of the milder types of hypothalamic suppression come from a paper by Prof. Jerilynn Prior, which I’ll link to in the show notes. In the paper, Professor Prior explains that hypothalamic suppression is not a disorder, but rather it’s the brain’s adaptive, intelligent response to protect the body from pregnancy when it would not be safe to have one.

That’s really quite different from polycystic ovary syndrome or PCOS, for which the obstacle to ovulation is essentially high androgens or testosterone, which directly interfere with the communication between the brain and the ovaries. So, in this case, it’s not about the brain making a smart decision. Instead, the brain-ovary communication is disrupted by the high testosterone.

PCOS usually shows up as long cycles or long gaps between bleeds, like having only three to four periods in a year. And those cycles could have a shortened luteal phase or, more commonly, they could be anovulatory. Only rarely will PCOS cause full amenorrhea or complete lack of periods because there’s usually a fair amount of estrogen around. And when there’s estrogen, the uterine lining builds up. That’s why, with PCOS—and less so with hypothalamic suppression— your doctor will probably talk about how you need something to protect the uterine lining or induce a bleed.

All right. Now, as you can imagine, the treatment for PCOS is quite different from the treatment for hypothalamic suppression. So, it’s pretty important to land on the right diagnosis. To help you get there, let’s compare and contrast the two situations. And there’s a visual of this compare-and-contrast in the video version of this podcast.

Both situations can present with absent or irregular periods or cycles. And both can have polycystic-looking ovaries on ultrasound or not, because “polycystic ovaries” really just means that follicle maturation and ovulation have not yet occurred in that cycle. That’s not specific to PCOS at all. For more on this, see Episode 3 of the podcast: PCOS cannot be diagnosed or ruled out by ultrasound. It’s also, of course, entirely possible to have the hormonal condition of PCOS (high androgens) but have normal-looking ovaries. That tends to happen in older women who have fewer follicles.

The main difference between the two situations—hypothalamic suppression and PCOS— starts with the fact that PCOS (by definition!) is associated with some degree of androgen excess, usually with androgen symptoms like hirsutism (as in, facial hair) or strong jawline acne. The symptoms are enough to gauge high androgens. Testosterone is not always high on a blood test. Although it can be. In contrast, hypothalamic suppression does not cause androgen excess, although there can still be, in some cases, post-pill acne or the mild facial or body hair that is normal for some people, depending on ancestry. And that can confuse the picture.

The next major difference is that PCOS—or at least the insulin-resistant type of PCOS— is associated with insulin resistance, showing up with biomarkers like high triglycerides, ALT, and sometimes a high fasting insulin. Although insulin is a little tricky to test. See my book about that. Whereas hypothalamic suppression will typically show no signs of insulin resistance. Quite the opposite, in fact. There could be a too-low fasting insulin.

Finally, with PCOS, the LH-to-FSH ratio is often high, at greater than 2-to-1, while with hypothalamic suppression, the ratio is typically low. And that’s because a high baseline level of LH is a key aspect of PCOS pathophysiology in many cases, and some PCOS treatments (such as cyclic progesterone therapy) work, in part, by lowering LH.

So, if your doctor orders a blood test for LH and FSH, make sure it’s timed to day 2 or 3 of your cycle—if you have a cycle—or, if you don’t have a cycle and therefore have to test on a random day, be cautious interpreting the result. You don’t want to accidentally measure your pre-ovulatory LH surge, which would show artificially high LH. You’ll know that’s what’s happened if you end up getting a period approximately two weeks after the high LH reading. So, you should wait two weeks to interpret your LH result.

Finally, it could happen that you have hypothalamic suppression against a background of PCOS or a background tendency to high androgens. In other words, your ovulation could currently be suppressed by undereating, and so you’re in a low-hormone, anovulatory state. But once you start eating more and your ovaries kick back into action, you could get pushed into a high-androgen anovulatory state. That “layering” or combination of hypothalamic suppression with PCOS is not super-common, but it is something to watch for.

Finally, just a few words about treatment. For hypothalamic suppression, the treatment is to convince your hypothalamus that all is well. In most cases, that means eating more—a lot more. And being fully nourished in every way, including protein, fats, and all the micronutrients. That could sometimes mean correcting a deficiency like zinc or iodine. Recovery might also require training less, resting more, and just generally feeling safer and better about the world.

And, even then — even once you’re doing everything right—you still might not get a period for several months. Maybe six months. That’s because there’s a lag time with periods. And what you do now can lead to better periods in a few months. That lag time is also true for PCOS, but the treatment for PCOS is quite different.

For starters, for PCOS, you’ll need something to lower androgens or testosterone. Conventionally, that’s the pill. But natural anti-androgen treatments include things like zinc, inositol, and cyclic progesterone therapy. Link in my bio to an article about cyclic progesterone therapy.

With PCOS, you’ll also need to address the underlying driver of androgens, or what I’ve described as the functional types of PCOS, such as post-pill, adrenal, inflammatory, or insulin-resistant PCOS. The insulin-resistant type of PCOS is, of course, the most common, and (as mentioned) will show up with high triglycerides, ALT, or a high fasting insulin on a blood test sometimes. By identifying and then reversing insulin resistance, you should be able to further lower your testosterone and achieve regular periods.

For more about assessing and treating insulin resistance, see my metabolism book, because there is no one-size-fits-all treatment for insulin resistance. Instead—as with many aspects of health — it can involve a little troubleshooting.

All right. I hope that’s been helpful, and thanks so much for listening! Or watching. Please share and leave a review. You can also leave a comment on the YouTube video or on the article associated with this episode at LaraBriden.com. And I’ll see you next time when I’ll share some new insights into premenstrual mood symptoms.