Pigs are considered as one of the potential resources for xenotransplantation because of physiological similarities with humans. Especially, SLA (Swine Leukocyte Antigen) genes are associated with immune responses and PERVs (Porcine Endogenous Retroviruses) are related with possible infection with exogenous viruses, which have been important issues for xenotransplantation. In this study, SLA class I gene (SLA-1, SLA-3 and SLA-2) alleles have been characterized in a herd of miniature pigs. Also, PERV insertional variations were investigated in six different pig breeds. As the results, three SLA class I haplotypes were identified in the miniature pig populations. Investigation of PERV insertion using eleven PERV loci (3 PERV-A, 6 PERV-B and 2 PERV-C) indicated that there are variations among breeds and among individuals. These results will give valuable information for designing effective breeding schemes, especially for xenotransplantation researches.