DQ alpha and beta DNA probes of the human major histocompatibility complex (MHC) were hybridized to restriction enzyme-digested genomic DNA with the aim of establishing a correspondence between the polymorphisms recognized by classical serology and DNA restriction fragment length polymorphisms (RFLP). In DR homozygous human cell lines, three distinct PstI fragments were recognized by the DQ alpha probe and four PstI fragments were recognized by the DQ beta probe. Each fragment was associated with a different group of DR antigens. Three allelic forms of either DX alpha or beta genes were identified, but none showed any strong association with DR or DQ. Family segregation analysis at the DNA level further confirmed the DR linkage of the DQ alleles in estimations of gene frequencies of different alleles of DQ alpha, DQ beta, DX alpha and DX beta. Evidence was presented that the DQ alpha and DQ beta allelic forms described at the DNA level correspond to polymorphic determinants at the cell surface which can be defined serologically or in cellular assays. Our data suggest that the HLA-DQ subregion-encoded alloantigens should be defined at the individual alpha and beta chain levels.