Pesticides and chemical fertilizers are widely used in agriculture to increase crop productivity among farmers. However, exposure to pesticides will give potential risk to human health. The aim of this study was to analyze the frequency of micronucleus (MN) and binucleus (BNu) formation in buccal cells from farmers who were exposed to pesticides using the MN assay. Buccal swabs were collected from the farmers in Tanjung Karang (n = 32) and Kelantan (n = 43) using wooden tongue depressor. A structured questionnaire was used to obtain demographic data of the farmers. Cytogenetic analysis was carried out by Acridin Orange (AO) staining 0.0025% (w/v). The frequency of MN and BNu as the biomarkers for cytogenetic damage was observed by using a fluorescence microscope. Comparison of frequency of MN and BNu is conducted in two areas namely Tanjung Karang, Selangor and Kelantan because of the agricultural activity and the type of pesticides used are different. Results showed that the frequencies of both MN and BNu among farmers in Tanjung Karang were significantly higher (p < 0.05) compared to farmers in Kelantan. Meanwhile, for the socio-demographic factors (age, smoking status, working period), MN and BNu frequencies among farmers in Tanjung Karang were also significantly higher (p < 0.05) as compared to farmers in Kelantan. While in the aspect of pesticide exposure, the frequencies of MN and BNu showed no significant difference between the frequency of pesticide spraying (p > 0.05) and the practices of PPE (Personal Protective Equipment) (p > 0.05). This may suggests that cytogenetic changes were not influenced by these factors. In addition, correlation study shows positive correlation between the frequency of MN with the pesticide exposure of farmers in Tanjung Karang (p > 0.05, r = 0.015) and Kelantan (p > 0.05, r = 0.0158). Besides, the frequency of BNu also has a positive correlation with the pesticide exposure among farmers in Tanjung Karang (p > 0.05, r = 0.036) and farmers in Kelantan (p > 0.05, r = 0.013). Hence, this present study demonstrated that exposure to pesticides increased the formation of MN and BNu among farmers and the prolonged use of pesticides may induce genotoxicity and DNA damage to human