The use of molecular typing methods for defining human leukocyte antigen (HLA) Class I and Class II alleles is now commonplace. Molecular methods offer a greater accuracy than traditional serological methods (1 –5 ) which is reflected in many disease and transplantation studies (6 –9 ). This chapter describes a polymerase chain reaction sequence-specific primer (PCR-SSP) typing system that is applicable to the identification of all HLA class I and class II alleles, as well as alleles from non-HLA loci (10 ,11 ) . PCR-SSP is also variably known as allele-specific PCR or amplification refractory mutation system (ARMS).