Southern hybridization analysis of the ovine major histocompatibility complex (MHC) (MhcOvar) class I1 region, using sheep-specific probes for the DQAl, DQA2, DQB and DRA loci, has revealed extensive polymorphism. DQAl and DQAP had eight and 16 alleles respectively, DQB had six and DRA had three alleles. Little information was derived from the DRB locus owing to extensive cross-hybridization between the DRB probe and the DQB locus. Differences in allele frequency between breeds were revealed. At the DQAl locus a null allele (DQAl-N) was observed with a frequency of between 27% and 45%, making this the most common DQAl allele in all breeds examined. The frequency of DQA1-N homozygotes was between 11% and 18%, raising questions as to the functional significance of the DQAl gene. Linkage analysis between the D Q A l , DQAZ, DQB and DRA loci did not reveal any recombination.