Male genital tract birth defects have been associated in previous studies with several prenatal exposures to environmental and dietary risk factors. The purpose of this study was to explore the association between hypospadias and cryptorchidism, and the dietary habits of an agricultural population in Italy. A population-based case-control study was conducted in the Sicilian Province of Ragusa. Cases (n = 90) and controls (n = 202) included births for the period 1998-2002. Data on dietary habits of the mothers, as well as health-related social, occupational and environmental exposures prior to and during the index birth, were collected through interviews. Adjusted odds ratios (OR) were calculated by logistic regression after adjustment for confounding variables. Increased ORs were observed for mothers of children with hypospadias who, during pregnancy, frequently consumed fish (OR = 2.33 [95% confidence interval (CI) 1.03, 5.31]) and market-purchased fruit (OR = 5.10 [95% CI 1.31, 19.82]). For cryptorchidism, increased risk was observed in mothers consuming liver (OR = 5.21 [95% CI 1.26, 21.50]), and smoked products (OR = 2.46 [95% CI 1.15, 5.29]). For the two malformations pooled together, increased risk was associated with maternal consumption of liver (OR = 4.38 [95% CI 1.34, 14.26]) and with frequent consumption of wine (OR = 1.98 [95% CI 1.01, 3.86]). This study suggests that some maternal dietary factors may play a role in the development of congenital defects of the male reproductive tract. In particular, our data indicate that further research may be warranted on the endocrine-disrupting effects resulting from the bioaccumulation of contaminants (fish, liver), pesticides (marketed fruit, wine) and/or potentially toxic food components (smoked products, wine, liver).