Plasma probes of outbred and inbred strains of guinea pigs were investigated by agarose high voltage electrophoresis and isoelectrofocusing in PAGE for polymorphism of the complement proteins C4, C2 and factor B of the alternative pathway. In breeding experiments mode of inheritance and linkage to the GPLA system was studied. The polymorphic complement proteins C4 (with the allelic structural genes C4F(fast), C4S(alow), C4S1 and C4o(deficient)) factor B (with the common alleles BfF and BfS) and C2 (with the frequent alleles C2B(basic), C2A(acidic), and C2A1) are closely linked together. In inbred strains haplotypes of the composition: C4F-BfS-C2A1 or alternatively C4S or S1-BfF-C2B were found. The mode of inheritance of C2A and its linkage to C4 and Bf is a matter of further breeding studies. All three complement proteins are linked to the GPLA system as shown by family studies with well characterized and GPLA-typed inbred strains and outbred animals.