Background We investigated associations of area-level deprivation with obstetric and perinatal outcomes in a large population-based routine dataset. Methods We used the data of n = 827,105 deliveries who were born in hospitals between 2009 to 2016 in Bavaria, Germany. The Bavarian Index of Multiple Deprivation (BIMD) on district level was assigned to each mother by the zip code of her residential address. We calculated odds ratios (ORs) with 95% confidence intervals (CIs) for preterm deliveries, Caesarian sections (CS), stillbirths, small for gestational age (SGA) births and low 5-minute Apgar scores by BIMD quintiles with and without adjustment for potential confounders. Results We observed a significantly increased risk for preterm deliveries in mothers from the most deprived compared to the least deprived districts (e.g. OR [95% CI] for highest compared to lowest deprivation quintile: 1.06 [1.03, 1.09]) in adjusted analyses. Increased deprivation was also associated with higher SGA and secondary CS rates, but with lower proportions of stillbirths, primary CS and low Apgar scores. When one large clinic with an unusually high stillbirth rate was excluded, the association of BIMD with stillbirths was attenuated and almost disappeared. Conclusions We found that area-level deprivation in Bavaria was positively associated with preterm and SGA births, confirming previous studies. In contrast, the finding of an inverse association between deprivation and both stillbirth rates and low Apgar score came somewhat surprising. However, we conclude that the stillbirths finding is spurious and reflects regional bias due to a clinic which seems to specialize in termination of pregnancies.