Mancozeb is a widely used broad-spectrum fungicide known to be genotoxic and induces tumors in rodents at various sites. Pendimethalin is a member of family dinitroanaline of herbicides. Pendimethalin are well known to be more or less toxic to all living organisms. In this study, we investigated whether mancozeb and pendimethalin induce micronucleus and apoptosis in CHL (Chinese hamster lung) cells through flow-cytometry analysis for high throughput. We identified mancozeb (20, 40, 80 ug/ml) and pendimethalin (5, 10, 20 ug/ml) mediated micronuclei formation and apoptosis in a dose dependent manner. We evaluated an increase of micronuclei formation and apoptosis by flow-cytometry analysis and microscopy analysis. We identified that MMC (mitomycin) induced micronuclei formation as positive control and negative control (DW) has no effect on CHL cells. We demonstrated that mancozeb and pendimethalin may induce micronuclei formation and apoptosis in CHL cells. We also suggest that flow-cytometry analysis could be efficient high-throughput method for quantifying the formation of micronuclei.