A total of 21 clones of acyclovir (ACV)-resistant (ACV(r)) herpes simplex virus type 1 (HSV-1) and 23 clones of penciclovir (PCV)-resistant (PCV(r)) HSV-1, emerging during serial passages in the presence of ACV or PCV, were isolated under conditions excluding contamination of resistant mutants in the starting virus culture, and their mutations in the thymidine kinase (TK) and DNA polymerase (DNA Pol) genes were analyzed comparatively. Mutations in the TK genes from ACV(r) mutants consisted of 50% single nucleotide substitutions and 50% frameshift mutations, while the corresponding figures for the PCV(r) mutants were 4 and 96%, respectively (P < 0.001). Eight of the 21 ACV(r) clones, but none of the 23 PCV(r) clones, had mutations in DNA Pol. Only nucleotide substitution(s) could be detected in the DNA Pol gene, as the gene is essential for virus replication. Therefore, the results for the DNA Pol mutants are concordant with those for the TK mutants in that a single nucleotide substitution was commonly observed in the ACV(r), but not in the PCV(r), mutants. These results clearly point to differential mutation patterns between ACV(r) and PCV(r) HSV-1 clones.