Abstract Background Estimating the true risk of fetal malformations attributable to the use of medications is difficult and perception of risk by health professionals will impact their counseling and treatment of patients who need medication during pregnancy. The objective of this study was to assess the perception of the teratogenic risk of 9 commonly and 3 rarely prescribed drugs among general practitioners and specialists in obstetrics/gynecology. Methods All 811 general practitioners in the Region of Southern Denmark and all 502 specialist obstetricians/gynecologists in Denmark as a whole were invited to participate in the study based on an online questionnaire. Medians and interpercentile ranges of the perceived background risk and perceived risks for each of the drugs were included in the questionnaire. Results One hundred forty three (18 %) general practitioners and 138 (27 %) obstetricians/gynecologists participated. Estimates provided by the participants were generally in accordance with current knowledge of drugs with established safety during pregnancy. Perceptions of risks associated with warfarin and retinoid exposure were severely underestimated. Conclusions Understanding of teratogenic background risk and specific risks associated with in utero exposure to 12 different drugs generally approached the established knowledge. The risk associated with warfarin and retinoid exposure was severely underestimated by both groups of health care professionals, while general practitioners specifically overestimated the risk of sertraline and citalopram to some extent. In Denmark, general practitioners can prescribe antidepressants, and even minor misconceptions of the teratogenic potential of citalopram and sertraline may be of clinical relevance. In Denmark, systemic retinoids can only be prescribed by a dermatologist, and warfarin treatment is only rarely initiated in women of the fertile age without involvement of specialists in internal medicine. Hence, the active knowledge on the teratogenic potential of these drugs is likely to be less accurate among general practitioners and obstetricians/gynecologists; although still of clinical importance since these specialists are largely involved in the counselling of pregnant women.