The major histocompatibility class II DQ molecules are dimeric glycoproteins involved in antigen presentation to CD4(+) T cells. In the current work, we have performed the molecular analysis of the goat Cahi-DQA1 gene. Sequencing of the Cahi-DQA1 cDNA revealed a single 768bp open reading frame. The alignment of this sequence with its bovine and ovine DQA1 counterparts revealed a remarkable degree of nucleotide identity (92-93% for the most similar bovine and ovine sequences). Moreover, we amplified a region including the 3'-end of intron 1, exon 2 and the 5'-end of intron 2. We identified seven Cahi-DQA1 alleles that likely correspond to four different allelic lineages. The alignment of these seven Cahi-DQA1 alleles revealed the existence of 23 amino acid polymorphic sites, seven of which (alpha(10), alpha(55), alpha(56), alpha(68), alpha(69), alpha(71) and alpha(76)) are highly polymorphic with at least three amino acid substitutions. Ten of the 23 polymorphic amino acid sites were included in the peptide binding region and consequently they might play a crucial role in immunological processes modulating disease pathogenesis.