To determine the sex differences in chronic energy deficiency (CED) among adolescents in the context of patrilineal and matrilineal societies in Northeast India. Cross-sectional, community-based study of the Hmar patrilineal society and the Khasi (War and Khynriam) matrilineal society. Mizoram and Meghalaya in Northeast India. In total, 1733 adolescent boys and girls aged 9-16 y: Khynriam Khasis (n = 1005), War Khasis (n = 305) and Hmars (n = 423). Weight, height, and socio-economic characteristics. Body mass index (weight in kg/height in m2) was used for assessing CED relative to the international reference values. The overall prevalence of CED was significantly greater in boys than in girls. The sex differences in the prevalence of CED were 5, 10 and 6% points in the Khynriam Khasis, War Khasis and Hmars, respectively. Allowing for age and socio-economic variables, the risks of CED were about 1.82 (95% CI 1.14-2.90), 1.83 (95% CI 1.19-3.33) and 1.78 (95% CI 1.10-3.25) times greater in boys than in girls among the Khynriam Khasis, War Khasis and Hmars, respectively. Using logistic regression analysis, the prevalence of CED was negatively associated with family income across study populations. No significant association was found between CED and religion. Patrilineal and matrilineal forms of society were not reflected in the prevalence of CED among adolescents. Subject to further studies of the research problems concerning the nutritional status of adolescents, girls fare better than boys with respect to the prevalence of CED.