Menstrual cycle and vaccine side effects: study

Author: Jessica Lloyd
Senior Vulvovaginal Specialist Naturopath | BHSc(N) | ISSVD, ISSWSH, BSSM, ATMS

Last reviewed: July 2, 2026

Where you are in your menstrual cycle when you get a vaccination might change how you feel afterwards. A new study of 1,474 people who track their periods found that those vaccinated against COVID-19 in the follicular phase – the first half of the cycle, when oestrogen is rising – had about 35% higher odds of reporting at least one side effect than people vaccinated in the luteal phase, the progesterone-led second half.

The work, led by the London School of Hygiene & Tropical Medicine and published in npj Women’s Health in June 2026, is the first to flip the usual question around: instead of asking how vaccines affect periods, it asks how the phase of your menstrual cycle might shape vaccine side effects and your immune response.¹

Before anyone reaches for their calendar, this is early, observational, self-reported data, it is specific to COVID-19 vaccines, and it is absolutely not a reason to delay any vaccine. But it is an interesting nudge towards something we have suspected for a long time – that the hormonal shifts of the menstrual cycle reach far beyond the uterus.

What did the study actually find?

The team ran a survey through the period-tracking app Clue in late 2021 and early 2022, then matched people’s answers to the cycle data they had already been logging. Of everyone who responded, 1,474 had tracked enough of their cycle to be sorted reliably into the follicular or luteal phase at the time of their vaccination.¹

Two clear signals came out. First, follicular-phase vaccination was linked to roughly 35% higher odds of reporting any side effect (odds ratio 1.35).¹ Second, people vaccinated in the follicular phase went a median of 35 days longer before catching COVID-19 (200 days versus 165), which hints at stronger or longer-lasting protection – though the number of infections was small, so the researchers are careful not to over-read it.¹

The side-effect pattern was not a tidy on-off switch at the phase boundary. Reporting climbed through the late follicular phase, dropped sharply just after ovulation, then rose again to a second peak in the late luteal phase – which the authors think may reflect premenstrual symptoms getting tangled up with vaccine after-effects. Across the whole cycle, though, side effects were more likely after a follicular-phase vaccination.¹

Why would your cycle change how you respond to a vaccine?

The short version: your immune cells listen to your sex hormones. Neutrophils, dendritic cells, macrophages, T cells and B cells all carry receptors for oestrogen and progesterone, so when those hormones rise and fall across the month, immune behaviour shifts with them.^1,3

Broadly, oestrogen tends to act as a context-dependent immune enhancer, while progesterone is more of a relative immune suppressant. In the follicular phase, oestrogen is climbing, which fits with a livelier reaction to a vaccine – more soreness, more fatigue, more of the achy, run-down feeling that usually means your immune system is getting on with the job. In the luteal phase, progesterone dominates and tends to dampen things down.^1,3

This sits alongside what we already knew about sex and vaccines. Women and people assigned female at birth tend to report more side effects after vaccination and often mount stronger antibody responses than men – differences that have been pinned in part on sex hormones for years.³ What this study adds is the suggestion that the difference is not fixed; it may move with the cycle.

Lead author Poppy Cooper raises the obvious caveat: we cannot yet tell whether follicular-phase people are mounting a bigger immune response, or are simply more sensitive to the aches and tiredness a vaccine injection brings, since oestrogen and progesterone influence pain perception too. Untangling those two will take studies that actually measure hormone levels and antibodies.¹

How this connects to your vagina and wider hormonal health

This study is not about the vagina directly, but it lands squarely on something we talk about constantly: your hormones and the menstrual cycle are a whole-body operating system, not just a uterine one. The same oestrogen and progesterone swings that thicken your endometrial lining, shift cervical mucus and change vaginal tissue and pH across the month are also tuning your immune system.

That oestrogen-immune link is part of why your vaginal environment is not static. Oestrogen feeds the glycogen that your protective Lactobacillus bacteria thrive on, which is one reason vaginal symptoms can ebb and flow with your periods. When oestrogen is out of balance – see our piece on relative oestrogen excess – the knock-on effects can show up in mood, skin, breasts and the vaginal microbiome alike.

In our clinic, we see how powerfully cycle timing colours how people feel day to day – energy, mood, vaginal comfort, even how heavily they react to ordinary stressors – and immune factors. None of that surprises us. What is encouraging here is researchers finally treating the menstrual cycle as a real biological variable worth measuring, rather than messy background noise to be controlled away.

The important limits

This is a strong question well asked, but it is a first step, and the researchers say so plainly. A few things to keep in mind:

It is observational and self-reported, so it shows an association, not cause and effect.
The survey was filled in around eight months after vaccination on average, which can blur memory of exactly what happened and when.
No one measured actual hormone levels or antibody responses, so the mechanism is still informed guesswork.
It looked only at COVID-19 vaccines. Whether the same holds for flu, human papillomavirus (HPV) or anything else is unknown.
The infection numbers were too small to make any confident claim about protection.

Cooper is clear that the findings should not be read as a reason to time your vaccine around your cycle. The right time to get any recommended vaccine is when it is offered to you.

Frequently asked questions

Should I plan my vaccines around my menstrual cycle?

No. This single observational study is not a basis for scheduling jabs by cycle phase, and the researchers say so directly. Get any recommended vaccine when it is offered.

Does this mean side effects are worse, or that the vaccine works better, in the follicular phase?

It is not yet clear. More side-effect reporting in the follicular phase could reflect a stronger immune response, greater sensitivity to aches and fatigue, or both. The study could not separate these.

What is the difference between the follicular and luteal phases?

The follicular phase is the first half of your cycle, starting with your period, when oestrogen rises towards ovulation. The luteal phase is the second half, after ovulation, when progesterone dominates. If no pregnancy occurs, the cycle resets and your period begins again.

Are vaccine side effects dangerous in either phase?

The side effects discussed here are the usual mild, short-lived ones – sore arm, tiredness, aches. Reporting more of them is not a sign of harm. If you ever have a severe or unexpected reaction, seek medical care.

Does the COVID-19 vaccine affect my periods?

Earlier research found a small, temporary increase in cycle length after vaccination, mostly when the dose fell in the follicular phase, and it settled within a cycle or two.² It is minor and not a reason to avoid vaccination.

What this means for you

The practical takeaway is small and reassuring: if you tend to feel rough after a jab, the phase of your cycle might be part of the story, and that is normal hormonal biology doing its thing. It is not a flaw, and it is not a reason to skip or reschedule anything.

If your symptoms across the month feel bigger than ordinary cycle ups and downs – persistent vaginal discomfort, recurring infections, or changes you cannot explain – that is worth proper investigation. A comprehensive vaginal microbiome test can show what is actually growing down there, and you are always welcome to book an appointment to work through hormonal or microbiome questions with us.

This is general information, not a substitute for personalised medical advice.