Pesticides are used in agriculture to protect crops but represent at the same time a potential risk to farmers and environment. The aim of this work is the evaluation of 54 subjects occupationally exposed to pesticides and 30 subjects as a control group using the quantification of DNA damage level by means of the alkaline Comet assay and the evaluation of repair processes. Damage index Comet assay (DICA) and damage index repair assay (DIRA) were studied in 27 pesticide applicator workers, 27 non-pesticide applicators and controls. Our results show that both exposed groups revealed significant increase in DICA when compared with controls (P < 0.0001), as well as in DIRA (P < 0.0001). However, the spraying group exhibited a marginally significant difference in DICA (P = 0.05) when years of exposure are considered and a significant difference (P < 0.05) when the personal protective equipment used by individuals was taken as a comparison factor. The influence of confounding factors on the genotoxic effects of occupational exposure to pesticides was investigated and no significant differences were observed considering age, gender, smoking and alcohol consumption in relation to DICA and DIRA. Since DNA damage is an important step in events leading from carcinogen exposure to cancer disease, our study highlights the potential health risk associated with agrochemical exposure in developing countries with vast cultivated areas, such as Argentina.