Pesticide exposure possesses risk of genotoxicity to humans, particularly farmers. Despite accumulating evidences linking genotoxicity to pesticide exposure, epidemiological studies to address pesticide toxicity in occupationally exposed farmers in Malaysia remain underreported. Thus, this study was aimed to determine the presence of nuclear abnormalities through the assessment of micronucleus (MN) and binucleus (BNu) frequencies in exfoliated buccal epithelial cells from farmers who were exposed to pesticides. A cross-sectional study of farmers among different agricultural activities farmers in Bachok and Pasir Puteh, Kelantan, North East of Peninsular Malaysia was done to evaluate the presence of nuclear abnormalities and its correlation with their health status and farming activities. Analysis of buccal cells revealed that the frequency of MN was significantly higher (p < 0.05) in farmers as compared to controls. In contrast, no significant difference (p > 0.05) was observed for BNu frequency in between groups. Correlation analysis showed that apart from a significant (p < 0.05) and positive correlation between the duration of fertilizers exposure and frequencies of MN (r = 0.42, P = 0.001) and BNu (r = 0.37, P = 0.02), no other correlation of various confounding factors on the formation of MN and BNu were observed. In conclusion, pesticide and fertilizers exposure may contribute to the promotion of nuclear anomalies among Malaysian farmers who are engaged in mixed plantation activities. Further assessment of larger populations is important to address and overcome the potential risk of pesticide-induced genotoxicity.