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Population affinity estimation is frequently assessed from measurements of the cranium. Traditional models place individuals into discrete groups―such as Hispanic―that often encompass very diverse populations. Current research, including this study, challenges these assumptions using more refined population affinity estimation analyses. We examine craniometric data for a sample of individuals from different regions in Antioquia, Colombia. We first assessed the sample to understand intraregional variation in cranial shape as a function of birthplace or a culturally constructed social group label. Then, pooling the Colombian data, we compare cranial variation with global contemporary and prehistoric groups. Results did not indicate significant intraregional variation in Antioquia; classification models performed poorly (28.6% for birthplace and 36.6% for social group). When compared to other groups (American Black, American White, Asian, modern Hispanic, and prehistoric Native American), our model correctly classified 75.5% of the samples. We further refined the model by separating the pooled Hispanic sample into Mexican and Guatemalan samples, which produced a correct classification rate of 74.4%. These results indicate significant differences in cranial form among groups commonly united under the classification “Hispanic” and bolster the addition of a refined approach to population affinity estimation using craniometric data.