In recent years, pharmacogenomics have received much attention from the increased expectations for so-called order-made medicine. It is experientially clear that inter-individual differences exist in the degree of efficacy and occurrence of adverse effects. These inter-individual differences are observed not only among anticancer chemotherapeutics but in almost all drugs. Several studies have revealed that genetic factors are involved in these inter-individual differences. To date, the relationships have been revealed between adverse effects of some anticancer drugs and polymorphisms of drug metabolizing genes. Such relationships include 5-FU and DPYD gene, methotorexate and MTHFR gene, irinotecan and UGT 1A1 gene and 6-MP and TPMT gene. By using information on these polymorphisms, it will be possible to predict the occurrence of adverse effects before using anticancer drugs. In particular, information on polymorphisms related to the possibly adverse effects of irinotecan is now given in its package leaflet. This means that order-made medicine is a step closer. In this review, we discuss the relationships between polymorphisms of genes and the adverse effects of anticancer drugs. Furthermore, we want to suggest the direction of further pharmacogenomic studies with an eye to the realization of order-made medicine.