Digital rights group the Electronic Frontier Foundation (EFF) says women using period tracking apps must ensure they know how their data is being used.
It comes in the wake of the reported decision in the US to overturn the 1973 Roe v Wade legal ruling – which would make abortion illegal in 22 states.
There are fears that menstrual tracking apps could be used to punish those seeking a termination.
Some of these apps share data with third parties.
Exactly what the apps do with the period data is unclear, but some third parties feed that information back to the big tech companies like Google, Meta and Amazon.
Cooper Quintin, senior staff technologist at the EFF, told the BBC: "We strongly suggest that the developers of period tracking apps start thinking about the amount of data they are storing about their customers, and especially the ways that data could one day be used or misused in the future to cause harm, or be a tool of surveillance.
"Anyone working with user data, especially in the reproductive health space right now, should be thinking about what they can do to minimise the amount of data they collect and hold, and the length of time they hold that data."
Period trackers have been extremely popular with women trying to get pregnant, because the tools claim to predict ovulation days. Others use it for tracking menopause, and it is estimated the "femtech" market will be worth more than £40bn globally by 2025.
Flo, the most popular period tracker on the market, has more than 100 million users. It asks women to input intimate information such as how heavy their bleeds are, if they had unprotected sex, or have low libido.
Women with any privacy concerns could check the small print, where it says the women's health app would not share any details about "cycles, pregnancy, symptoms notes and other information that is entered by you".
However, from 2016 to 2019, the company was found to have passed on certain health details of its users to big tech firms. Flo said it was "solely for analytical purposes" – but some women were angry.
Now, with the possible reversal of the Roe v Wade ruling which legalised abortion in the US, women in the country who might find themselves seeking an illegal abortion are wondering if their menstrual cycle data could be used against them by law enforcement.
Tech outlet Protocol reported that in the case of subpoenas, companies can push back on providing individual user data, but they hand it over about 80% of the time.
The team at the Swedish "digital contraceptive" app Natural Cycles told the BBC this is a huge topic of conversation, and gave their users some reassurances.
"Unlike period tracking apps, Natural Cycles is an FDA-cleared [US Food and Drug Administration] birth control app – a medical device with very strict data privacy standards.
"All data stored on the app is safe and will be protected. Natural Cycles has always protected each user's data and will continue to."
Rhian Lewis, who runs a support group called the Online Abortion Resource Squad on social media platform Reddit, told the BBC it has seen a surge in traffic to the group's r/Abortion page since the leak of a possible US Supreme Court decision at the start of the week.
She said: "Typically, r/Abortion averages more than 500,000 page views per month, from about 20 to 30,000 unique visitors. Our daily unique visitor count doubled from Monday to Tuesday."
All of these women are not asking about privacy concerns though – most are asking about how to access a clinic, which resources they need, and legal information.
Ms Lewis continued: "For digital privacy questions around abortion we would direct people to the Digital Defense Fund, as this is their speciality.
"The issue of this data is threefold: Who in your life can find out you had an abortion? What corporations would have access to your menstrual history, and what would they do with it? Are there legal implications for you if law enforcement has that information?" Ms Lewis says.
"We can't make decisions for people, and we know that people use digital tools to look after themselves and to try and understand their bodies, especially when they want to try and avoid becoming pregnant.
"But the data can be shared in many ways, and it's really important that people are informed and aware of the implications, even the ones that seem far-fetched or inconsequential at first."