Does your menstrual cycle affect how vaccines work?

New research using Clue data suggests that how far along you are in your menstrual cycle when you get a vaccine could affect whether you experience side effects, and possibly how long the vaccine protection lasts.

Hormones influence your immune system

If you've ever noticed you're more likely to get sick at certain points in your cycle, there may be a biological reason for this.

Scientists have long known that women have stronger immune responses than men (1). They catch fewer infections, fight off colds, flu, and COVID-19 more quickly, and produce more antibodies after vaccination, including against COVID-19.

It's not all good news, though; a stronger immune response can mean the body overreacts to potential immune threats, explaining why women make up 80% of autoimmune disease diagnoses, and why they're more likely to report vaccine side effects (2).

A major reason for this difference? Hormones. 

While the effects of reproductive hormones can vary depending on the circumstances, estrogen is often linked to stronger immune responses, including more side effects and stronger antibody production after vaccination, while progesterone and testosterone can often dampen immune responses (3).

Women, especially between puberty and menopause, have much higher levels of estrogen and progesterone, while men have higher testosterone levels.

But these hormones don't just differ between men and women. They also shift across each menstrual cycle, with estrogen dominating the first half of the cycle (the follicular phase) and progesterone dominating the second half (the luteal phase). 

So, if hormones influence different vaccine responses, and these same hormones are changing across your menstrual cycle, the obvious question is: does the timing of your cycle affect how you respond to a vaccine? Does it matter whether you happen to be vaccinated on day 5 or day 22? Until now, this question has remained almost entirely unexplored.

What we did

Our research team, a collaboration between scientists from the London School of Hygiene & Tropical Medicine, Oregon Health & Science University, Brunel University London, the Institute of Evolutionary Sciences in Montpellier, and Clue, set out to find out whether where you are in your cycle matters for your reaction to the COVID-19 vaccine. 

We ran a survey in the Clue app asking users when they received their first COVID-19 vaccine dose, which side effects they experienced, how severe they were, and whether they'd contracted COVID-19 since.

Next, we matched their responses with their Clue cycle data to pinpoint exactly which day of their cycle they were vaccinated. 

Why this matters: Because Clue users had already been tracking their cycles in Clue before being vaccinated, we could use real tracking data rather than simply relying on memory.

Of the 1,474 Clue users in the analysis:

• 760 were vaccinated in their follicular phase, when estrogen is dominant

• 714 in their luteal phase, when progesterone is dominant

What we found: The cycle vaccine connection

You're more likely to experience side effects if you get the vaccine in the first half of your cycle.

Participants vaccinated in the follicular phase had 35% higher odds of reporting side effects following vaccination compared with those vaccinated in the luteal phase.

This was still true when we excluded people vaccinated just before or in the first few days of bleeding, giving us confidence that the side effects were from the vaccine, not from PMS (premenstrual symptoms) or their period.

Cycle timing might affect protection from infection—but more evidence is needed

We also examined whether the cycle phase at vaccination predicted how long protection lasted. Those vaccinated in the follicular phase went on average 35 days longer before becoming infected (200 vs 165 days).

This hints at better protection, possibly because they were vaccinated when estrogen levels were higher. But with only 82 infections in the analysis, we can't draw firm conclusions yet. More research is needed.

Why are we only finding this out in 2026?

Historically, the menstrual cycle has been ignored in medical research, assumed to be too complicated or not important enough to study. This study and others like it show that this assumption is wrong. 

The menstrual cycle has body-wide impacts, shaping immune function, pain perception, mood, and much more beyond just reproduction. It's an important biological variable, and science is finally catching up.

What this means for your next vaccine

This does not mean you should time your vaccinations to a specific phase of your cycle. Getting vaccinated when you can is far more important than worrying about cycle timing. This is the first study to look at how menstrual cycles affect vaccines, and a lot more research is needed before any recommendations can or should be made.

But studies like this are able to exist because people track their cycles. Clue's user-generated data helped us to uncover these relationships between cycles and vaccines, which would have gone unnoticed otherwise.

What’s next? We'd like to explore this with confirmed ovulation data, giving us a much more precise picture of how specific hormonal shifts interact with vaccine response. 

Interested in how Clue data is helping researchers better understand menstrual and reproductive health? You can explore all of Clue’s peer-reviewed papers, ongoing studies, and research collaborations on the Clue Scientific Research page.