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Human milk oligosaccharides (HMOs) protect against infection and promote growth and cognitive development in breastfeeding children. Non-genetic factors which influence HMO composition in breastfeeding mothers in rural Africa have not been investigated. We undertook a cross-sectional study to determine the association between HMO profiles and non-genetic maternal factors and childrens sex in Ugandan mother-children pairs. Human milk was collected from 127 breastfeeding mothers by manual expression. HMO analysis was by high performance liquid chromatography. The proportion of each HMO per total HMO concentration was calculated. Spearmans correlation and Mann-Whitney U test were used to assess the relationship between individual HMOs and maternal factors and infant sex. Nineteen HMOs were assayed. The prevalence of secretor and non-secretor status, based on the proportion of mothers with high milk concentrations of 2FL and LNFP 1, was 80.3 % and 19.7 %, respectively. In secretor mothers, 2FL, DFLac and LNFP I constituted > 57 % while in non-secretor mothers LNT and LNFPII constituted 46.9 % of the measured total HMOs. The median 3SL concentration in milk of all mothers of male children was significantly higher than that in all mothers of female children. The median DFLac concentration in all mothers was significantly higher in multiparous mothers compared to primiparous mothers. Higher FDSLNH and lower LNH concentrations were observed in overweight secretor and non-secretor mothers, respectively. Median concentrations of LNFP I and DSLNT were …