We determined the CYP2D6 alleles in cell lines derived from 81 Japanese individuals with the CYP450 probe arrays using an Affymetrix GeneChip apparatus. Sequencing of the CYP2D6 exons from these same cell lines was performed to determine the accuracy of the allele calls by the Affymetrix probe array. Comparison of the results showed differences in the data from three cell lines for the CYP2D6(*)10 alleles between these two methods. These results indicated that the CYP450 probe array must be utilized cautiously for typing CYP2D6(*)10 alleles, which are frequently observed in the Japanese population.