Genetic diversity within the DQA genes of the major histocompatibility complex (Mhc) of cattle is characterised by multiple polymorphic loci that can vary in number between haplotypes. Previous analysis of the second exon sequences derived from genomic BoLA DQA3 genes identified two distinct families, DQA3*01 and DQA3*02. In this report, we describe the nucleotide and predicted amino acid sequences of the entire coding region of three transcribed BoLA DQA3 genes representing each of these families. These data provide additional evidence that the BoLA DQA3 locus is distinct from BoLA DQA1 and BoLA DQA2. In addition, the amino acid sequence of DQA3 genes from the two families is shown to differ by 35 out of the 254 amino acids. Putative locus-specific amino acid sequence motifs within the transmembrane and intracytoplasmic domains of DQA genes are shown to differ between the DQA3*01 and DQA3*02 genes. Phylogenetic analysis reveals a genetic distance that is considerably larger than that seen between orthologous Mhc allelic families. These data are consistent with either an extremely divergent family of DQA3 genes or an allele at an additional BoLA DQA4 locus.