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The rules and structure of human culture impact health as much as genetics or environment. To study these relationships, we combine ancient DNA (n=230), skeletal metrics (n=391), paleopathology (n=606), and dietary stable isotopes (n=873) to analyze stature variation in Early Neolithic Europeans from North Central, South Central, Balkan, and Mediterranean regions. In North Central Europe, stable isotopes and linear enamel hypoplasias (LEH) indicate high environmental stress across sexes, but female stature is low, despite polygenic scores identical to males, and suggests cultural factors preferentially supported male recovery from stress. In Mediterranean populations, sexual dimorphism is reduced, indicating male vulnerability to stress and no strong cultural preference for males. Our analysis indicates that biological effects of sex-specific inequities can be linked to cultural influences at least as early as 7000 years ago, and culture, more than environment or genetics, drove height disparities in Early Neolithic Europe.