Detection of hepatitis A virus (HAV) has been greatly aided by the development of polymerase chain reaction (PCR) technology. However identification of genetic variants requires sequencing PCR products, which necessarily limits the extent of the HAV genome that can be analyzed (typically 2%). Identification of HAV strains detected by PCR is important not only to rule out contamination of test samples in the diagnostic laboratory, but also to locate the geographic origin of the virus. We have explored alternatives to sequencing to achieve these goals. Our findings indicate that digestion of PCR products from two noncontiguous segments of the HAV genome encompassing 765 nucleotides (approximately 10% of the genome) by the restriction endonucleases Hinf I and Alu I can distinguish the common tissue culture adopted strains of HAV from stool isolates. The resolution can be greatly enhanced by combining single strand conformation polymorphism (SSCP) analysis with restriction enzyme digestion, when most of the seventeen strains analyzed could be identified.