Populations with histories of outbreeding tend to be taller even in the face of seemingly unchanged health and nutritional circumstances, while inbreeding generally results in a negative correlation between body dimensions and level of inbreeding. Populations that have experienced a positive secular trend in stature and maturation typically have histories of higher outbreeding rates in combination with improved nutritional, health, and economic conditions, suggesting a genetic-environment interaction. In general, Middle American Indians have not experienced a secular trend in stature, nor a substantial increase in their standard of living, but they have experienced varying degrees of admixture with Spanish and African populations since the Spanish Conquest. The relationship between estimated gene flow and variation in several anthropometric dimensions is thus considered in indigenous Mesoamerican populations. Available data on height, sitting height, craniofacial dimensions, and admixture rate of Indian populations from southern Mexico, Guatemala, and Honduras were assembled from the literature. The population mean data on 3,371 adults from 23 populations for males and 18 for females were analyzed by regression with anthropometry as the dependent variable, and log10 of admixture as the independent variable. Admixture was ⩽ 28.9% in this study and is suggestive of a primarily traditional Indian cultural and economic base. The results suggest that populations with higher admixture tend to be taller, and that the increase in stature is due to greater subischial length in both sexes. A decrease in nasion-menton height, and an increase in nasal breadth, nasal height, and the nasal index is suggested for the dimensions of the craniofacial complex. These data thus suggest changes in anthropometric dimensions and proportions associated with gene flow, apparently in the absence of improved health and nutritional conditions.