Nilotinib, a second-generation tyrosine kinase inhibitor of BCR-ABL, has shown superior efficacy compared with imatinib for the treatment of chronic myelogenous leukemia (CML). Unconjugated hyperbilirubinemia has been the most frequent adverse event with laboratory abnormality observed in clinical trials of nilotinib. The homozygosity for uridine diphosphate glucuronosyltransferase (UGT) 1A1*28 polymorphism has been reported to increase the risk of nilotinib-induced unconjugated hyperbilirubinemia in Caucasians. However, the frequency of UGT1A1*28 is low in Asians, including Japanese. On the other hand, the UGT1A1*6 allele mutation, which is extremely rare in Caucasians, is more frequent than the UGT1A1*28 allele in the Japanese population. Herein, we present a patient with CML who developed grade 3 unconjugated hyperbilirubinemia after being treated with nilotinib. We found that the patient was heterozygous for both UGT1A1*28 and *6. Our findings suggest that the compound heterozygosity for UGT1A1*28 and *6 could be a cause of unconjugated hyperbilirubinemia during nilotinib treatment.