We analyzed the distribution of HLA class II alleles and haplotypes in one Na-Dene (Athabaskan) group from British Columbia (Canada) by PCR amplification of the DRB1, DQA1 and DQB1 second exon sequences. We extended the typing of the DRB1 in an Amerindian group (Penutian) from British Columbia. The presence of the alleles DRB1* 0405, *0407 and *0410 only in Na-Dene and alleles DRB1*0408, *1301*1302, *1304, *1305, *1502 and *1601 only in Amerindians suggests separate origins of these two groups. There were fifteen different DRB1/DQA1/DQB1 haplotypes. One unique haplotype previously reported in Native Americans was found. Thirty-four per cent of Athabaskans presented Native American haplotype DRB1*1402/DQA1*0501/DQB1*0301. In addition, the results of this study are compatible with previous evidence with mitochondrial (mtDNA) polymorphisms indicating that Amerindians and Na-Dene populations derived from different migrations from Asia.