Objective To analyze potential biosocial factors in consanguineous unions according to the level of consanguinity and its spatial distribution in South America. Methods The data used came from the Latin American Collaborative Study of Congenital Malformations. Information on 126,213 nonmalformed newborns out of 6,014,749 births was used. This information was collected between 1967 and 2011 at 204 hospitals in 116 cities in 10 South American countries. The spatial scan statistic was performed under a model of nonhierarchical k‐means segmentation, based on statistically significant clusters, areas with levels of high, medium, and low consanguinity were determined. Results Consanguinity in South America is heterogeneously distributed, with two groups of high consanguinity, in northwestern Venezuela and southeast of Brazil, and two clusters of low consanguinity located in the south of the continent, mainly Argentina. The socio‐demographic factors associated with consanguinity influence the population structure in areas of high consanguinity. Conclusions This study demonstrates that consanguinity in the South American continent is strongly associated with a greater magnitude of poverty in the area of high consanguinity. Am. J. Hum. Biol. 28:405–411, 2016. © 2015 Wiley Periodicals, Inc.