Abstract Background One of the groups that is most vulnerable to the COVID-19 pandemic is pregnant women. They cannot choose to refrain from care; they and their children are at risk of severe complications related to the virus; and they lose comfort and support as clinics prohibit their partners and as societal restrictions demand isolation from friends and relatives. It is urgent to study how this group is faring during the pandemic and we focus here on their health-related worries. Methods A longitudinal survey at a Swedish hospital starting 6 months before (16 September 2019) and continuing during the COVID-19 outbreak (until 25 August 2020). A total of 6941 pregnant women and partners of diverse social backgrounds were recruited. Ninety-six percent of birth-giving women in the city take early ultrasounds where recruitment took place. Sixty-two percent of the women with an appointment and fifty-one percent of all partners gave consent to participate. Results Pregnant women experienced dramatically increased worries for their own health, as well as for their partner’s and their child’s health in the beginning of the pandemic. The worries remained at higher than usual levels throughout the pandemic. Similar, but less dramatic changes were seen among partners. Conclusions There is a need for heightened awareness of pregnant women’s and partners’ health-related worries as a consequence of the COVID-19 pandemic. Related feelings, such as anxiety, have been linked to adverse pregnancy outcome and might have long-term effects. The healthcare system needs to prepare for follow-up visits with these families.