The aim of this study was to analyze in families with SLE for the presence of linkage and the structure and transmission of haplotypes containing alleles for the low-affinity Fcg receptors. The Fcg receptor polymorphisms FcgRIIA-131R/H, FcgRIIIA-176F/V and FcgRIIIB-NA1/2 and a polymorphism in the FcgRIIB gene were genotyped with RFLP, allele-specific PCR or pyrosequencing. Individual SNPs and haplotypes were tested for linkage in multicase families and for association using contingency tables, transmission disequilibrium test and affected family-based control groups in Swedish and Mexican singlecase families. No linkage or association could be detected using the FcgR polymorphisms in the multicase families. However, an association was found for both FcgRIIA-131R and IIIA-176F alleles in the single-case families, but not for IIIB or IIB. Allelic association to SLE was found for a haplotype that included both risk alleles, but not in haplotypes where only one or the other was present. We propose that FcgRIIA-131R and FcgRIIIA-176F are both risk alleles for SLE transmitted primarily, but not exclusively on a single major haplotype that behaves functionally in a situation similar to that of compound heterozygozity.