C4A null genes were determined by RFLP (Taq I) and SSO-probing on PCR-amplified C4-DNA in 51 Scandinavian patients with systemic lupus erythematosus (SLE) and 124 controls. Associations of the alleles DRB1*0301, DQA1*0501, DQB1*0201 had previously been found in this SLE group, as well as increased frequency of HLA-DRB1 and -DQ homozygosity. The frequency of the allele C4A*Q0 was increased among the patients (RR = 2.3, P = 0.0172). The SSO-probing revealed additional cases of C4A*Q0 homozygotes among the controls, leading to diverging RR values for C4A*Q0 homozygotes depending on the technique used. The RFLP method gave an RR of 9.7 (P = 0.0028), while the SSO-probing resulted in an RR of 4.8 (P = 0.0153), demonstrating that unprecise characterization of C4A*Q0 in a relatively small material has great effect on the calculated RR. Multiple 2 x 2 tests were performed in an attempt to detect the strongest association of the alleles DRB1*0301, DQA1*0501 and C4A*Q0 (in linkage disequilibrium). These comparisons showed a trend towards stronger association for DAQ1*0501 and DRB1*0301 than for C4A*Q0, and no interaction between the HLA alleles and the allele C4A*Q0. This may suggest that HLA class II molecules themselves and/or an unknown susceptibility gene located near the DQA1 and DRB1 loci are involved in the pathogenesis of SLE.