An increased frequency of the S allele of Properdin factor B (BfS) was found amongst 162 patients with multiple sclerosis (MS) compared with 470 normal controls. This increase was shown to be due to a strong linkage disequilibrium (LD) between BfS and HLA—Dw2 in 77 patients typed for both systems (Δ= 3.84%, P= .0002). The same LD was demonstrated amongst 100 normal controls (Δ= 2.24%, P= .0049) and 31 patients with idiopathic demyelination of the peripheral nervous system (IDPN). A total of 70 haplotypes with HLA‐Dw2 were encountered (40 MS, seven IDPN and 23 normal controls) and all contained BfS. In the MS patient group, a much weaker association was noted between BfS and HLA—B7 suggesting either that the Bf locus is much closer to the HLA—D than the HLA—B locus or (and) that HLA‐D and Bf products selectively interact (perhaps on the surface of B lymphocytes) with evolutionary advantage or disadvantage resulting from certain allelic combinations. Strong associations between BfS1 and HLA—Bw21 (P= .0000) and BfF1 and HLA—B18 (P= .0001), both previously reported, were confirmed in the current study. No increase in the frequency of a glyoxalase (GLO) allele was found amongst the MS patients and no LD was encountered between HLA—Dw2 and a GLO allele. The possibility that the HLA—Dw2, BfS disequilibrium has resulted from a selective advantage conferred on the general community but at the expense of increasing susceptibility to MS should be considered.