The antigens for the MNS blood group system are Glycophorins A and B (GPA,GPB), products of the GPA gene family. The existence of close to 40 variant phenotypes of this blood group system has been documented by serological analyses. Here is summarized the molecular basis for a large number of variants, including all the variants of the Miltenberger complex and several isoforms of Sta; also, Dantu, Sat, He, Mg, and deletion variants Ena, S-s-U- and Mk. The diversity is based predominantly on gene recombinations, namely unequal homologous recombinations and/or gene conversions, often coupled to pre-mRNA splicing. Most rearrangements occurred between GPA and GPB alleles, and were confined to hot-spots within the 4 kb region coding for the extracellular domain. The homologous region in GPE, the third member of the gene family, was involved only rarely. Sites of the variant epitopes are mapped to new intra- and inter-exon junctions or to patches of previously silenced sequences that become expressed following recombination.