Opportunities to assess morphological allometry in small-bodied human populations are rare. The foragers of the Later Stone Age of the South African Cape are characteristically small-bodied. Previous studies have shown that during the period of ca. 3500 to 2000 years BP (uncalibrated 14C dates), the regional population shows transient reduced stature, body mass, and cranial size, a pattern that has been tentatively tied to demographic pressure on resources. This study examines the relationships among cranial size (centroid size) and body size (femoral length, femoral head diameter, and bi-iliac breadth) during the second half of the Holocene (N = 62). Reduced major axis regression indicates negative allometry of cranial centroid size with body size. Residuals (from ordinary least squares regression of cranial centroid size on body size) are regressed on radiocarbon date to examine temporal changes in the relationship between cranial and body size. Cranial and pelvic sizes are most conserved through time, while more ancient skeletons possess shorter femora and smaller femoral heads. The relationship between cranial centroid size and femoral length shows larger and more variable residuals at more recent dates, indicating a greater or more variable disassociation between cranial size and stature relative to more ancient skeletons. A similar, but nonsignificant relationship exists between cranial size and bi-iliac breadth. These results provide insights into the use of aspects of body size and proportionality in the assessment of health in past populations. Am J Phys Anthropol 2012. © 2012 Wiley Periodicals, Inc.