Aim: To assess the safety of proton pump inhibitors during pregnancy.Methods: Fifty‐one pregnant women exposed to proton pump inhibitors around the time of conception or during pregnancy were compared with 13 327 controls without exposure to any prescribed drug in a population‐based study based on The Pharmaco‐Epidemiological Prescription Database of North Jutland and the Danish Hospital Discharge Registry.Results: Three babies with malformations were found among 38 women exposed to proton pump inhibitors from 30 days before conception to the end of the first trimester. No cases of stillbirth were recorded. Crude relative risks of malformation, low birth weight and preterm delivery were 1.6 (95% CI: 0.5–5.1), 1.8 (95% CI: 0.2–13.0) and 2.3 (95% CI: 0.9–6.0), respectively.Conclusions: In this population‐based follow‐up study, we found no substantially elevated risk in terms of malformations, low birth weight or number of preterm deliveries in pregnancies exposed to proton pump inhibitors. However, further monitoring is warranted in order to establish or rule out a potential association between the use of proton pump inhibitors and increased risk of either cardiac malformations or preterm birth.