The genetic polymorphism of vitamin D binding protein (DBP) and of properdin Factor B (BF) was determined in unrelated Namibian San and Khoi, and in South African Blacks, Caucasoids and Cape Coloureds. Alleles have been confirmed by segregation patterns in family studies. The DBP phenotypes were identified by isoelectric focusing on ultrathin polyacrylamide gels and the BF phenotypes were identified by electrophoresis on 1% agarose gels; both methods were followed by immunofixation. The DBP and BF allele frequencies for all population groups were found to be in accordance with Hardy-Weinberg equilibrium. DBP*1S and BF*S allele frequencies in the San, Khoi and Blacks were similar; their frequency was far lower than in Caucasoids. The frequencies of the DBP*1F and BF*F were also similar in the San, Khoi and Blacks; however, the allele frequency was much higher in these groups than in Caucasoids. These differences were statistically significant (P < 0.001).