The frequencies of Properdin factor B allotypes were studied in 54 multiple sclerosis patients and 58 healthy control subjects, and the association of various phenotypes with HLA-Dw1 and Dw2 antigens (found with decreased and increased frequency in MS patients, respectively) was further studied. SS genotype was found in 76% of MS patients and 63% of control subjects (n.s.) F types (FS + FF) were found to be strongly associated with HLA-Dw1 in control subjects (P less than 0.0014), whereas neither SS nor F containing types were associated with Dw2. The findings support the concept of a hypothetical MS resistance factor in the HLA gene area.