Abstract Background Since the presence of a birth defect is often a primary outcome in drug‐safety studies among pregnant women, researching the validity of data collection methods is imperative. The aim of this study is to compare self‐reported birth defects in infants by mothers with the information provided by general practitioners (GP (singular) or GPs (plural)). Methods Mothers who participated in the Dutch Pregnancy Drug Register reported information about possible birth defects of their infants via questionnaires. GPs were approached to provide information on possible birth defects of the same infants. All reported birth defects by mothers and GPs were blindly coded using the International Classification of Diseases, Tenth Revision (ICD‐10) index and EUROCAT‐classified as either a minor or major birth defect. Differences in reported birth defects between participants and GPs were assessed. Results Participants and GPs ( N = 551) reported 67 and 53 birth defects respectively, leading to a total of 120 birth defects among 65 infants. When both the GP and the participant reported a birth defect, 76.9% of these birth defects ( N = 60) were coded with an identical ICD‐10 code. Information on the absence of a birth defect and the presence of a major birth defect was identically reported by the GP and the mother in almost all cases (98.2%). Of the major birth defects reported by the GP, 67% could be matched with information provided by the participant, for 33% contradicting information was reported. Conclusion Self‐reported questionnaire data on infants' birth defects from mothers yield fairly similar information compared to information obtained through GPs. Future studies should validate the accuracy of self‐reported birth defects by mothers more extensively to improve the quality of drug safety studies during pregnancy.