Empirical evidence demonstrates associations between socioeconomic or environmental area deprivation and public health. To measure such structural effects, deprivation indices have been developed in the UK initially. Meanwhile their application is increasingly discussed in Germany, however with little attempts to adapt the concept to national conditions. In this paper, we develop a model of area deprivation differentiating between material, social and ecological deprivation effects. We apply structural equation modelling to endogenously estimate the latent deprivation dimensions as well as their relative impact on the health outcome, accounting for potential measurement errors and controlling for health care infrastructure. We use data at the level of German municipal associations (n=4,491) for the years 2013 and 2016, if available. We find that differences in material (β material =−0.168, p<0.001) and social deprivation (β social =−0.249, p<0.001) as well as ecological damage (β ecological =−0.077, p<0.001) explain part of the health differences in Germany. The social dimension is paramount in a health context. Moreover, deprivation dimensions cancel out each other and combining them in one overall index blurs the diverse picture of area deprivation in Germany. The small area analysis illustrates, that different strategies in environmental-, education- or health policy are necessary to reduce deprivation in different regions.