High prevalence and severity of rheumatoid arthritis (RA) with an early age of onset have previously been described in Alaska Native and American Indian (AN/AI) populations. The contribution of HLA-DRB1 alleles encoding a similar amino acid sequence, referred to as the shared epitope (SE), to RA risk is well recognized in multiple populations worldwide. DRB1*1402 allele is the major SE-encoding allele in AN/AI populations. However, DRB1*1402 is highly prevalent in healthy Alaska Natives of Southeast Alaska (AN), with no significant difference from RA patients, indicating this allele alone is not informative for defining genetic risk and non-human leukocyte antigen (non-HLA) genes are likely important in AN. We sought to deep resequence the human major histocompatibility complex (MHC) to characterize the single-nucleotide polymorphism (SNP) haplotypes within this region in RA cases and controls in AN. Approximately 99 kb of the MHC was resequenced with 95 amplicons throughout this region. Thirty-four cases and 74 controls were examined. A total of 696 SNPs were discovered from 85 of the selected 95 amplicons. Disease association signals were detected for nine of the 95 amplicons analyzed. Increased risk of RA was associated with five amplicons in the class I, class II or class III region and resistance to disease with four amplicons in the class I region. Our results indicate that non-HLA MHC genes and/or unknown exogenous factors likely modulate risk of RA in the AN population.