The dog has served traditionally as a model for marrow and organ transplantation. A key component of any study of transplantation is histocompatibility typing of donors and recipients. Towards the development of a less expensive, more simplified typing system within canine families, a new highly polymorphic microsatellite marker for the canine Major Histocompatibility Complex class II region was isolated and characterized. In addition, we report on the application of class I and class II microsatellite-based markers for following the inheritance of the alleles within the canine analog of the human HLA loci, DLA, through multi-generation pedigree.