Using discriminant function analysis, classification accuracies for ancestry and sex in white and black South Africans were compared using North American (FDB), African groups in Howells (HDB), and South African (SADB) databases in FORDISC 3.0. (FD3). Twenty-four standard linear measures were collected from a total of 86 black and 101 white crania obtained from the Pretoria Bone Collection. White and black South Africans classified 73% correctly in FDB, 55% correctly in HDB, and 71% correctly in SADB. The percentage of atypical cases was higher with FDB than SADB. In all three databases, misclassification occurred more with sex than ancestry revealing differences in sexual dimorphism between population groups. Broad ancestral differences may explain low misclassification rates for ancestry. FD3, with a modern South African reference sample, can assist South African anthropologists to standardize methodology and to justify procedures for estimating ancestry.