The dog has been an important model for solid organ and hematopoietic stem cell transplantation for over 30 years. Fundamental to the continuing usage of the model is the development of molecular-based histocompatibility typing of donors and recipients. Previous histocompatibility typing methods used in the dog have not been precise enough to identify dog leukocyte antigen (DLA)-matched unrelated dogs. This study was undertaken to begin the process of identifying DLA-matched unrelated dogs. In this study polymerase chain reaction-single-stranded conformational polymorphism is used to separate alleles thereby allowing sequenced-based typing of the two most polymorphic class II genes described to date in the dog-DLA-DRB1 and DLA-DQB1.