MiV, MiV(J.L.), and Sta glycophorins specify the respective variant phenotypes of the human MNSs blood group system. We report that unequal but homologous crossing-over between alpha and delta glycophorin genes results in three hybrid genes encoding MiV, MiV(J.L.), and Sta glycophorins. Restriction mapping and allele-specific oligonucleotide hybridization grossly defined the third intron as the probable crossing-over site and showed that MiV and MiV(J.L.) genes are arranged in the same 5' alpha-delta 3' frame whereas Sta gene is in a reciprocal 5'delta-alpha 3' configuration. Genomic sequences spanning the extracellular domain exons 2 to 4 were amplified from each variant gene by polymerase chain reaction and determined by direct DNA sequencing. Comparison of nucleotide sequences encompassing the third intron showed that the three hybrid genes differed in location of crossing-over sites. The alpha-delta breakpoints in MiV and MiV(J.L.) genes were localized to the 3' end of the HindIII site downstream from exon 3 and to the 5' end immediately upstream from exon 4, respectively, whereas the delta-alpha breakpoint in Sta gene resided in between. An AAAGT sequence oriented in either forward or reverse direction was identified within the crossing-over region of each hybrid gene whose surrounding sequences bear a strong local strand asymmetry. The single nucleotide substitution in exon 4 of MiV and MiV(J.L.) genes (ACG [Thr] to ATG [Met]) demonstrated that the two genes differed in the delta glycophorin alleles that must have participated in the recombination.