Background and objectives: Evolutionary research on the sex ratio at birth (SRB) has focused on explaining variability within and between populations, and whether parental fitness is maximized by producing daughters or sons. We tested predictors of SRB in a low-income setting, to understand whether girls differ from boys in their likelihood of being born into families with the capacity to invest in them, which has implications for their future health and fitness. Methodology: We used data from a cluster randomized control trial from lowland rural Nepal (16 115 mother-child dyads). We applied principal component analysis to extract two composite indices reflecting maternal socio-economic and reproductive (parity, age) capital. We fitted mixed-effects logistic regression models to estimate odds ratios of having a girl in association with these individual factors and indices. Results: The SRB was 112. Compared to the global reference SRB (105), there were seven missing girls per 100 boys. Uneducated, early-marrying, poorer and shorter mothers were more likely to give birth to girls. Analysing composite maternal indices, lower socio-economic and reproductive capital were independently associated with a greater likelihood of having a girl. Conclusions and implications: In this population, girls start life facing composite disadvantages, being more likely than boys to be born to mothers with lower socio-economic status and reproductive capital. Both physiological and behavioural mechanisms may contribute to these epidemiological associations. Differential early exposure by sex to maternal factors may underpin intergenerational cycles of gender inequality, mediated by developmental trajectory, education and socio-economic status.