In this research we have used the MHC typing technologies we have developed forsheep, in dairy cattle. We have identified eleven alleles at the Bovine DQA2 locus to date,including two new sequences (Accession Numbers AF 388177 and AF388178). Thesegregation of these alleles has been assessed in large progeny groups derived from eight sires,covering two dairy breeds (Holstein-Friesian and Jersey). Preliminary evaluation revealsstatistically significant differences in mean somatic cell count for the progeny groups and a linkbetween particular alleles and increased or decreased somatic cell count in some sirelines.