Background: In a national perinatal health programme, we observed striking heterogeneity in the explanation of the most prominent risks across municipalities. Therefore we explored the separate contribution of several socio-demographic risks on perinatal health inequalities between municipalities and neighbourhoods. The study aims to identify perinatal health inequalities on the neighbourhood level across the selected municipalities, and to objectify the contribution of socio-demographic risk factors on pregnancy outcomes in each municipality by the application of the population attributable risk concept. Methods: Population based cohort study (2000-2008). Perinatal outcomes of 352,407 single pregnancies from 15 municipalities were analysed. Odds ratios and population attributable risks were calculated. Main outcomes were combined perinatal morbidity (small-for-gestational age, preterm birth, congenital anomalies, and low Apgar score), and perinatal mortality. Results: Perinatal health inequalities existed on both the municipal and the neighbourhood level. In municipalities, combined perinatal morbidity ranged from 17.3 to 23.6 %, and perinatal mortality ranges from 10.1 to 15.4%. Considerable differences in low socio-economic status between municipalities were apparent, with prevalences ranging from 14.4 to 82.5 %. In seven municipalities, significant differences between neighbourhoods existed for perinatal morbidity (adjusted OR ranging from 1.33 to 2.38) and for perinatal mortality (adjusted OR ranging from 2.06 to 5.59). For some municipalities, socio-demographic risk factors were s a strong predictor for the observed inequalities, but in other municipalities these factors were very weak predictors. If all socio-demographic determinants were set to the most favourable value in a predictive model, combined perinatal morbidity would decrease with 15 to 39 % in these municipalities. Conclusions: Substantial differences in perinatal morbidity and mortality between municipalities and neighbourhoods exist. ...