In recent years, the use of pesticides has intensified worldwide, and many countries have tended to neglect the potential toxic effects associated with the indiscriminate use of these substances. Many diseases, such as Hodgkin’s lymphoma, lung and prostate cancer, and autoimmune disorders, have been linked to the use of pesticides. The present study compared the DNA damage observed in rural workers from five different areas of the central Brazilian state of Goiás. We attempted to identify the factors that influence the patterns of genotoxicity found in 367 rural workers from the municipalities of Goiânia, Rio Verde, Montividiu, Jatai, and Silvânia. The DNA damage was assessed using comet assays, and the results were compared with the data on epidemiological variables, behavioral parameters, and the types of pesticide used. Significant variation was found in the level of DNA damage in rural workers from different municipalities, although no clear differences were observed in demographic or behavioral parameters. All the different classes of pesticides were related to similar levels of DNA damage, which indicates that other factors may be influencing the differences observed among the populations. A positive correlation was found between the level of DNA damage and the number of pesticides used per individual, which suggests potential synergistic effects of pesticide mixtures, which may enhance the risk of DNA damage. Rural workers from Goiânia and Silvania presented the highest levels of DNA damage. In addition to the quantity of pesticides and the synergistic effects of mixtures, the results of the present study would appear to point to genetic polymorphisms in detoxification genes (e.g., OGG1 and XRCC), which may determine variation in the general susceptibility of the different populations to DNA damage. This emphasizes the need for further research on the possible variation in genetic factors in the different groups of rural workers.