Balanites aegyptiaca (L.) Delile. is one of the priority indigenous fruit trees for rural communities in the West African Sahel. As part of a participatory tree domestication program in Niger, phenotypic variation in fruit and seed morphology was assessed in four natural populations in eastern Niger. Measured variables were weight of the fruit, seed coat and kernel; length and width of the fruit and seed (25 trees per population, 30 fruits per tree). Derived variables were the tree's coefficient of variation (CVs) for each measured variable, and two sets of factor scores from principal components analysis of tree means and CVs. ANOVA indicated significant variation in all measured variables due to trees nested in populations. ANOVA and simple linear regression indicated significant geographic variation in some variables: the drier parts of the sample region tended to have heavier fruits and kernels, longer/narrower seeds, and lower within-tree variability in fruit and seed width. Length and width were strongly correlated between fruits and seeds, fruit weight was moderately correlated with seed dimensions, and CVs of fruit weight and width were moderately correlated with the CV of seed width. Some hypotheses for the geographic variation are presented, and some practical implications of the correlations for tree domestication programs are discussed.