Narcolepsy has a 98% association with the DR2-Dw2/DQw1 haplotype. To establish if a disease-specific allele is present in narcolepsy, a cDNA library was made from a B-cell line from a DR2,4/DQw1,3 narcoleptic. Clones encoding the two expressed DR2 beta chains, along with DQw1 alpha and beta chains, were isolated and completely sequenced. The coding regions of these four genes were similar to published nucleotide and protein sequences from corresponding healthy controls, with some minor exceptions. The 3' untranslated region of one of the DR2 beta genes in the narcoleptic was extended by 42 bp. Complete sequences were not available for DQw1.2 alpha or beta from healthy individuals, but first domain nucleotide sequences showed only a single nonproductive difference in DQ alpha. Partial protein sequences of both DQ alpha and beta from published data were identical. Although the effects of minor differences cannot be ruled out completely, it is concluded that there are probably no narcolepsy-specific DR beta or DQ alpha/beta sequences, and that the alleles found in narcolepsy are representative of those found in the healthy population.