Natural selection for small adult body size may be directly linked to various factors that differ by global region. Indirect selection through early cessation of growth has been postulated for pygmy groups. Small adult body size was maintained throughout the Holocene by the ancestors of the KhoeSan groups, Later Stone Age hunter-gatherers who lived in the coastal and near-coastal regions of South Africa. Contextual information from 134 burials of juveniles (76 with radiocarbon dates) is combined with assessment of child growth. Both timing of cessation of growth and patterns of juvenile mortality are pertinent to questions about the possible selective value of smallness. Later Stone Age juveniles who had dental ages in the midteen years had not yet achieved adult size; hence, early cessation of growth is not evident. For the period between ca. 3800 and 1800 BP, which was a time of increased variability in adult body size, there are more burials of older juveniles. The variability in the mortality profile suggests fluctuations in the rates of juvenile mortality rather than consistently high rates. We conclude that small body size had been established by the Holocene, and we suggest that its maintenance is linked to direct rather than indirect selection.