In order to evaluate the previously published association between maternal use of selective serotonin re-uptake inhibitors (SSRI) and persistent pulmonary hypertension in the neonate (PPHN), we used data from the Swedish Medical Birth Register for the years 1997-2005. Infants were identified from discharge diagnoses, and maternal exposure to drugs from interviews performed in early pregnancy and from prescriptions from the antenatal care service. Putative confounders were studied: an increased risk for PPHN was indicated for high maternal age, for first parity, for maternal BMI, and possibly for maternal smoking. Adjusting for these variables and year of birth, an association between maternal use of SSRI and PPHN in births after 34 completed weeks was identified with a risk ratio of 2.4, 95%CI 1.2-4.3 when based on women who reported the drug use in early pregnancy. When a subgroup of the women were studied who also had prescriptions for SSRI from the antenatal care later in pregnancy, the risk estimate was 3.6, 95%CI 1.2-8.3. The risk estimates were lower than that described previously in the literature, but both estimates could come from the same about 4-5 times increased risk. The mechanism behind the association between SSRI and PPHN is unclear but an increased risk for respiratory problems after maternal use of SSRI is well known, and PPHN could be a rare part of this association.