The HLA genetic region consists of a large multigene complex which includes a number of highly homologous alpha and beta genes encoding class II polypeptides, clustered in three major loci, DP, DQ, and DR. Analysis of genomic polymorphisms at each of these loci is of considerable interest due to the role of particular structural polymorphisms in immune function, but this analysis has been hampered by difficulty in distinguishing between such highly homologous loci. We have identified locus-specific and exon-specific class II gene sequences in order to produce synthetic oligonucleotide probes which hybridize specifically to DQ beta genes. Two such oligonucleotide probes are described which are specific for the beta 1 and beta 2 exons of DQ (DC) beta, which identify DQ beta genes in digests of cellular DNA and which can be used to characterize restriction sites flanking the two oligonucleotide-specific regions. By sequentially hybridizing these probes in modified Southern analyses, we have been able to generate a tentative "restriction map" of a newly identified DQ beta allele from digests of total genomic DNA. This oligonucleotide mapping technique discriminates between two HLA-DQw3+ alleles, DQ3.1 and DQ3.2, permitting the recognition of structural polymorphisms with DQ beta which are highly associated with type I diabetes mellitus.