Pesticides have been considered as potential chemical mutagens; however, little is known about toxic and genotoxic effects during pesticide application in Zamora-Jacona, Michoacan State in Mexico. This study sought to determine DNA damage and cholinesterase activities inhibitions in 54 agricultural workers exposed to complex mixtures of pesticides vs. control group (26 individuals) using Comet assay in peripheral whole blood, micronucleus (MN) test in oral mucosa cells, Cytokinesis-blocked MN assay in lymphocytes (L-CBMNcyt) and measuring AChE and BChE activities in whole blood and plasma samples, respectively. Exposed subjects demonstrated significantly elevated levels of primary (Comet assay: tail intensity, tail length, tail moment, Olive tail moment) and permanent DNA damage (MN assay: in blood/buccal cells; frequencies of nuclear buds, binucleated cells, cells with condensed chromatin, karyorrhexis, pyknosis, and karyolysis). However, inhibition of cholinesterase activities (AChE and BChE) was not observed in the workers. Confounding factors including sex, age, BMI, working exposure period, protection level, smoking habit (cigarettes per day units), alcohol consumption (weekly), medication, were considered in the analysis. These combined techniques demonstrated usefulness in the health hazards risks pesticide exposure assessment and suggested the need for periodic monitoring together with the education and the training of occupational workers for the safe application of potentially harmful pesticides.