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Background: Proton-pump inhibitors (PPIs) are often needed in pregnancy due to the high rates of acid reflux. Previous studies did not include medical pregnancy terminations data, which may cause a bias toward the null hypothesis. We assessed the fetal safety of PPIs following exposure during gestation including data from medical pregnancy terminations. Methods: A unified computerized database was created by linking a computerized database of medications dispensed from 1998 to 2009 to all women registered in 'Clalit' HMO, southern district of Israel, with computerized databases containing maternal and infant hospitalization records from the district hospital. Rates of congenital malformations in PPIs exposed and unexposed pregnancies, as well as other adverse fetal effects were compared. Medical pregnancy termination data were included in the analysis. Results: A total of 114,960 (75%) infants were born during the study period to women registered at 'Clalit,' 110,783 of them were singleton pregnancies; 1,239 women had medical pregnancy terminations, of which 468 were performed due to fetal malformations. A total of 1,186 infants and abortuses had been exposed to PPIs during the first trimester of pregnancy. Exposure to PPIs was not associated with an increased risk of congenital malformations (adjusted OR 1.06; 95% CI = 0.84-1.33). Similarly, exposure to PPIs during the third trimester of pregnancy was not associated with increased risk of perinatal mortality, premature delivery, low birth weight, or low Apgar scores. Conclusions: Intrauterine exposure to PPIs was not associated with increased risk for congenital malformations, perinatal mortality, or morbidity. These results are strengthened with the inclusion of data from medical pregnancy terminations. [ABSTRACT FROM AUTHOR]