Background Gestational diabetes mellitus (GDM) occurs in 2–6 % of all pregnancies. We investigated whether area level deprivation is associated with a higher risk for GDM and whether GDM detection rates in deprived regions changed after the introduction of charge-free GDM screening in Germany in 2012. Methods We analyzed population-based data from Bavaria, Germany, comprising n = 587,621 deliveries in obstetric units between 2008 and 2014. Area level deprivation was assessed municipality-based using the Bavarian Index of Multiple Deprivation (BIMD), divided into quintiles and assigned to each mother based on her residential address. We estimated annual odds ratios (ORs) for GDM diagnosis by BIMD quintile with adjustment for maternal obesity, maternal age, migration background and single mother status. Results Women from the most deprived regions were less likely to be diagnosed with GDM before introduction of charge-free GDM screening (OR = 0.76 [95 % confidence interval: 0.66, 0.86] compared to least deprived areas), in 2008. In contrast, high area level deprivation was associated with significantly increased risk of GDM diagnosis in 2013 (OR [95 % confidence interval] = 1.15 [1.02, 1.29]). The OR was also elevated, although not significantly, in 2014 (OR [95 % confidence interval] = 1.05 [0.93, 1.18]). Conclusions The prevalence of GDM seems to have been underreported in women from highly deprived areas before introduction of the charge-free GDM screening in Germany. In fact, women living in deprived regions seem to have an increased risk for GDM and may profit from access to charge-free GDM screening.Gestational diabetes mellitus Area level deprivation Bavarian index of multiple deprivation Charge-free screening.