During the last decades, the focus of food and nutrition security research has shifted from issues of macro-level availability to problems of unequal access, and distribution within the household. Little systematic attention has however been paid to the role of family systems in household food allocation processes. This study focuses on the extent to which family relations, and particularly gender roles, in two Himalayan communities with different family systems influence intra-household food allocation, and the subsequent nutritional status of women of reproductive age (15–49). In-depth interviews were conducted with 15 Buddhist and 15 Hindu women, the latter belonging either to the higher Chhetri or lower Dalit castes. Additionally, anthropometric data of women were collected. Results show that women from Hindu families were worse off than women from Buddhist households in terms of nutritional status, which is due to different intra-household allocation patterns. Secondly, women's nutritional status varied over the reproductive life course. Women were most vulnerable during menses, pregnancy, and the post-partum period. Comparison with research conducted in the 1980s in this area suggests that the influence of family-level values and practices on women's nutritional status is slowly changing.