Widespread use of pesticides in agriculture represents a threat not only to the environment but also to human populations exposed to them. Many of these compounds are capable of inducing mutations in DNA and lead to several diseases including cancer. In the present study, cytogenetic damage in peripheral lymphocytes from 33 farmers of Oporto district (Portugal) exposed to pesticides was evaluated by means of micronuclei (MN), sister chromatid exchange (SCE) and chromosomal aberrations (CA). In addition, effect of polymorphic genes of xenobiotic metabolizing enzymes (GSTM1, GSTT1, GSTP1, CYP2E1 and EPHX1) was also evaluated. A non-exposed group from the same area and with same demographic characteristics without exposure to genotoxic compounds was studied and data obtained from both groups was compared. MN and SCE frequencies were significantly higher in the exposed group (P < 0.005). In what concerns CA results, no significant differences were observed. It was possible to relate a specific working environment (greenhouses) with higher levels of genetic damage. Use of personal protective equipment revealed to be important to prevent exposure and diminish genetic damage inflicted by pesticides. Allele frequencies of studied polymorphic genes obtained in this study are similar to the ones described by other authors for Caucasian populations. Despite the low number of subjects, results suggest that low mEH (microsomal epoxide hydrolase) activity as well as GSTT1 positive genotype are associated with increased cytogenetic damage.