Genetic susceptibility and environment exposures are associated risk factors in carcinogenesis. Gene polymorphisms that decrease the activity of detoxifying carcinogen substances may modify the effect of exposures. We investigated whether the polymorphisms PON1 rs662 (Q192R), and PON1 rs854560 (L55M) would be associated with embryonal tumors in Brazilian children. Blood samples from 163 children with embryonal tumors and 342 as control group were genotyped by TaqMAN real-time PCR assays. Logistic regression was used to evaluate the association between the polymorphisms of cases and controls groups, adjusted by skin color and age strata. When all tumors were taken together, the presence of the PON1 rs662 (Q192R) variant genotype (RR) was associated with an increased risk of developing embryonal tumors (OR = 2.80, 95 % CI 1.12-7.02). The presence of at least one variant PON1 rs662 R allele increased the risk of developing Wilms´ Tumor although without statistical power. However, it was observed a significant association of PON1 rs662 (Q192R) variant genotype (RR) with retinoblastoma (OR = 4.08, 95 % CI 1.13-14.97), whereas the PON1 rs854560 (L55M) polymorphism was not associated with any tumor. These results indicate that PON1 polymorphisms may have an influence on the risk of developing embryonal tumors.