Introduction and Aim Data from prescription databases are increasingly being used to study associations between maternal medications used in pregnancy and congenital anomalies. We therefore investigated the extent to which prescriptions reflect the actual use of medication during pregnancy, and whether medicines used during pregnancy are taken according to the prescribed dosage and duration. Methods We performed a cross-sectional study in a population-based congenital anomaly register (EUROCAT Northern Netherlands). We included 202 women who had at least one prescription during their pregnancy and who gave birth between 2009 and 2011. Compliance with the prescribed medication was verified by telephone interview. We calculated the compliance rates for several medication groups by dividing the number of mothers who confirmed they had taken the medication by the total number to whom it had been prescribed. Compliance was positive if the mother confirmed she took the medication, even if she only took one of several prescriptions from the same medication group. For each prescription taken, we also determined whether her use conformed to the prescribed dosage and duration. Results During the first trimester, the compliance rates ranged from 0.84 (for chronic diseases) to 0.92 (for pregnancy-related symptoms). Most of the medications actually taken were used at the prescribed dosage or lower. More than half of the medications actually taken were used for the duration prescribed or shorter. Conclusion Prescription records are generally a relatively reliable source of data for research into associations between medication use in pregnancy and congenital anomalies compared with other data sources. Pharmacy records of medication use in pregnancy might represent an overestimation, which should be taken into account. However, our results show that, except for 'corticosteroids, dermatological preparations'; 'ear, eye, nose and throat preparations'; and 'anxiolytics, hypnotics and sedatives', this overestimation generally ...