Thiopurine methyltransferase (TPMT) catalyses the S-methylation of thiopurine drugs. Low-activity phenotypes are correlated with several mutations in the TPMT gene. Polymorphisms of TPMT have been reported for Caucasians, African-Americans and Asians. Since ethnic differences have been demonstrated worldwide, it remains to be elucidated in Brazil. The Brazilian population is the result of five centuries of interethnic crosses between peoples from almost all continents as well as autochthonous Amerindians, all forming the fifth largest and one of the most heterogeneous populations in the world. The frequency of six allelic variants of the TPMT gene, *2 (G238C) (2.2%), *3A (G460A and A719G) (1.5%), *3B (G460A) (0.2%), *3C (A719G) (1.0%), *5 (0%) and *6 (0%) were determined in Brazilian subjects using polymerase chain reaction (PCR)-RFLP and allele-specific PCR-based assays. This study provides the first analysis of TPMT mutant allele frequency in a sample of the Brazilian population.