Background. We investigated the epidemiology of congenital malformations and childhood cancer. Procedure. By employing the cases of the Registry of Childhood Malignancies in Hokkaido Prefecture, Japan, from 1969 to 1996, the numbers of malignancies in cases (diagnosis at 0-14 years of age) with Down syndrome (DS), mental retardation (MR) excluding DS, luxatio coxae congenita (LCC), congenital heart disease (CHD) excluding DS, undescended testicle (UT), and cleft palate-lip (CPL) were calculated. Using the percentages of malignancies in the 2,349 cases without malformation, expected numbers of malignancies in the cases with the malformations were calculated. The observed numbers were statistically compared to expected ones. Results. In the DS cases, leukemia developed with a significantly high frequency, but no UT cases developed leukemia. No brain tumor was preceded by DS. This could not be explained only by early death from coexisting diseases such as CHD, insofar as the CHD cases without DS developed brain tumors more frequently than expected. The ratio of acute lymphoblastic leukemia (ALL) to acute nonlymphoblastic leukemia (ANLL) was different among the malformations. The MR cases developed ANLL more frequently than expected, whereas the CPL cases developed ALL more frequently. The distribution of the age at diagnosis for Wilms' tumor was different according to the underlying malformation. Conclusions. Malformations might have some fac- tors that inhibit or delay as well as promote the development of certain malignancies.