In order to assess possible human effects associated with glyphosate formulations used in the Colombian aerial spray program for control of illicit crops, a cytogenetic biomonitoring study was carried out in subjects from five Colombian regions, characterized by different exposure to glyphosate and other pesticides. Women of reproductive age (137 persons 15–49 yr old) and their spouses (137 persons) were interviewed to obtain data on current health status, history, lifestyle, including past and current occupational exposure to pesticides, and factors including those known to be associated with increased frequency of micronuclei (MN). In regions where glyphosate was being sprayed, blood samples were taken prior to spraying (indicative of baseline exposure), 5 d after spraying, and 4 mo after spraying. Lymphocytes were cultured and a cytokinesis-block micronucleus cytome assay was applied to evaluate chromosomal damage and cytotoxicity. Compared with Santa Marta, where organic coffee is grown without pesticides, the baseline frequency of binucleated cells with micronuclei (BNMN) was significantly greater in subjects from the other four regions. The highest frequency of BNMN was in Boyacá, where no aerial eradication spraying of glyphosate was conducted, and in Valle del Cauca, where glyphosate was used for maturation of sugar cane. Region, gender, and older age (≥35 yr) were the only variables associated with the frequency of BNMN measured before spraying. A significant increase in frequency of BNMN between first and second sampling was observed in Nariño, Putumayo, and Valle immediately (<5 d) after spraying. In the post-spray sample, those who reported direct contact with the eradication spray showed a higher quantitative frequency of BNMN compared to those without glyphosate exposure. The increase in frequency of BNMN observed immediately after the glyphosate spraying was not consistent with the rates of application used in the regions and there was no association between self-reported direct contact with eradication sprays and frequency of BNMN. Four months after spraying, a statistically significant decrease in the mean frequency of BNMN compared with the second sampling was observed in Nariño, but not in Putumayo and Valle del Cauca. Overall, data suggest that genotoxic damage associated with glyphosate spraying for control of illicit crops as evidenced by MN test is small and appears to be transient. Evidence indicates that the genotoxic risk potentially associated with exposure to glyphosate in the areas where the herbicide is applied for coca and poppy eradication is low.