Background When women are in a condition that requires medicines during pregnancy they have to balance the health benefits of the medical treatment against the potential risk of harming their unborn child. Too high teratogenic risk perceptions among pregnant women can lead them to stop taking the medicine, worsening the symptoms for the mother and even harming their foetus. Many women today who use over-the-counter and prescribed medicines have been shown to change their medical behaviour when they become pregnant. Objective To explore in depth the perceptions of medication use among women during their pregnancy. Setting The Capital Region of Denmark. Methods Participants were recruited from social network groups on Facebook and from participants in lectures and antenatal classes for pregnant women in two hospitals. Two focus groups interviews and three individual semi-structured interviews were conducted. The interview guides were based on existing literature and relatively unstructured, with an emphasis on open-ended questions. Interview transcripts were analysed using the phenomenological approach of meaning condensation. Main Outcome measure Pregnant women's' perceptions of medicine including aspects related to their safety feeling of medicines and perceived support from health care professionals. Results The women believed that it is less safe to take medicines during pregnancy, largely due to the risk of the child getting a disease in the future, but also due to the risk of malformation. Lack of clinical tests and uncertainty about how the unborn child reacts to medications were reported causes of these concerns. Most participants were concerned about using medicines and avoided them if possible, including over-the counter medicines. Conversations with physicians had a calming effect although the physicians appeared to be unclear in their guidance regarding dietary supplements. Some women received conflicting information on the Internet. Several suggestions were made about how to reduce uncertainties about the safety of taking medicines during pregnancy. Conclusion Many pregnant women are concerned about how to use medicines. To reduce these concerns and ensure the appropriate use of medicines during pregnancy, initiatives are needed to strengthen evidence-based advice from health care professionals, especially during the first trimester.