C4 allotype frequencies and their combination with factor B and C2 alleles (complotypes) were studied in a sample of the Spanish population in relation to MHC class I, class II and GLO alleles. The shorter genetic distances found for C4 between Spaniards and North Africans and the high frequency of extended HLA haplotypes (GLO*2) HLA‐DR3 F1C30 HLA‐B18 HLA‐Cw5 (HLA‐A30) and HLA‐DR7 S1C21 HLA‐Bw50 HLA‐Cw6 are consistent with a paleo‐North African ethnic origin (about 20000 years B.C.) of a part of present Spaniards (Iberians), and with the effect of racial admixture during late Moslem invasions (from the 8th to the 15th century). The complotype null alleles C4A*QO and C4B*QO may be under natural selection pressure when found incisposition, since they are never in the same haplotype in families. The underestimation of these C4 null alleles’frequencies in unrelated individuals as compared to genotyped families is shown to be a very likely event and a serious hindrance for C4‐disease association studies. We have not found any C4 duplications in the Spanish population; this may be due to sample size limitations or to the degree of admixture of our population. Strikingly, no positive linkage disequilibrium between C4A and C4B alleles is detected in unrelated individuals nor in families, although strong associations are maintained among Bf, C2, C4, HLA‐A, HLA‐B, HLA‐C and HLA‐DR markers. Assuming that all MHC polymorphisms have reached equilibrium, several explanations are proposed, including the possibility of no, different or additional natural selection mechanisms operating on some MHC class III genes (Bf, C2, C4 alleles combinations for most appropriate C3 convertases), as compared to those affecting class I and class II gene clusters (most advantageous