Rheumatoid arthritis (RA) is prevalent in Yakima Indians, a Native American tribe. HLA-DR4, the HLA specificity commonly associated with RA in Caucasians, is rare among the Yakima. Using a specific oligonucleotide probe that recognizes DR4 nucleotide sequences associated with RA, a rare HLA-Dw16 gene was identified in 83% of Yakima patients with RA and in 60% of Yakima control subjects. This shared sequence encodes a discrete class II epitope that is highly correlated with RA in both DR4 positive and DR4 negative individuals.