The major histocompatibility complex (MHC) class II molecules are heterodimeric cell surface glycoproteins important for antigen presentation to CD4+ T lymphocytes. Class II molecules of the pig MHC, termed SLA, identified so far include DR and DQ. Thus far, functional differences between products of different loci in SLalpha class II have not been well characterized. For detailed research on this issue, SLalpha-DRbeta1 and -DQbeta typings were newly developed by restriction fragment length polymorphism (RFLP) of the reverse transcriptase-polymerase chain reaction (RT-PCR) products. Using this method, several RFLP types were chosen from 13 CSK miniature pigs, and alloreactivities in two-way mixed lymphocyte culture (MLC) derived from these pigs were examined by cell proliferation assay using flow cytometry. The responses in MLC varied according to the degree of phenotype difference. In MLC from individuals of the same RFLP type in both SLA-DRbeta1 and -DQbeta, the proliferative responses showed slight reaction indicating that they were not so stimulated by each other. On the other hand, for the RFLP type-mismatching combination, the responses were strong indicating that they recognized each others alloantigens. The reactivity of only the DQbeta mismatching combination was as strong as those of only the DRbeta1 mismatching combination. These data indicate the important role of the DQ as well as DR molecule on alloreactivity in MLC.