The rules and structure of human culture impact health and disease as much as genetics or the natural environment. Studying the origins and evolution of these patterns in the archaeological record is challenging as it is difficult to tease apart the effects of genetics, culture, and environment. We take a multidisciplinary approach by combining published ancient DNA, skeletal metrics, paleopathology, and dietary stable isotopes to analyze cultural, environmental, and genetic contributions to variation in stature in four geographically defined populations of Early Neolithic Europe: North Central, South Central, Southern (Mediterranean), and Southeastern (Balkan) Europeans. In individuals from Central Europe, female stature is low, despite polygenic scores for height identical to males and to neighboring regions. Dietary and skeletal stress markers indicate environmental stress that is equal in both sexes, but the high stature sexual dimorphism ratio suggests that these stresses were exacerbated in females by cultural factors, likely associated with male preference and sex-biased allocation of resources. In contrast, shorter average stature in Mediterranean Neolithic populations have been previously reported to be associated with genetic differences; however, this is likely an artifact of residual population structure in the genome-wide association studies (GWAS). Instead, we suggest that reduced sexual dimorphism in the region indicates a degree of male vulnerability in response to general environmental stress. We conclude that while population-level stature trends may in some cases reflect genetic factors, differences in sexual dimorphism are largely driven by culture, or the interaction of culture and environment. Our analysis indicates that biological effects of sex-specific inequities can be linked to cultural influences at least as early as 7000 years before present. Understanding these patterns is key to interpreting the evolution of genetic and socio-cultural determinants of health and our results show that culture, more than environment or genetics, drove height disparities in Early Neolithic Europe.