Background The objective of this study was to analyse the association between area deprivation at municipality level and the prevalence of type 2 diabetes (T2D) and obesity across Germany, controlling for individual socioeconomic status (SES). Methods The analyses are based on a large survey conducted in 2006. Information was included from 39,908 adults aged 20 years or above. Area deprivation was assessed using the German Index of Multiple Deprivation (GIMD) at municipality level. About 4,700 municipalities could be included and assigned to a deprivation quintile. Individual SES was assessed by income and educational level. Multilevel logistic models were used to control for individual SES and other potential confounders such as age, sex and physical activity. Results We found a positive association of area deprivation with T2D and obesity. Controlling for all individual-level variables, the odds ratios for municipalities in the most deprived quintile were significantly increased for T2D (OR 1.35; 95% CI 1.12-1.64) as well as for obesity (OR 1.14; 95% CI 1.02-1.26). Further analyses showed that these associations were relatively similar for both men and women. Conclusions Based on a nationwide dataset, we were able to show that area deprivation at municipality level is significantly associated with the prevalence of T2D and obesity. It will be important to focus preventive efforts on very deprived municipalities.