The exponential growth in the production and consumption of engineered nanoparticles (ENPs) has raised concern about their environmental fate. ENPs accumulation in ecosystems is likely to pose threat to specific and non-specific targets. In this study a novel approach using flow cytometry was validated for detection of ENPs (ZnO and TiO2) uptake in live bacteria for several generations. These ENPs also induced frameshift mutation in S. typhimurium strains of Ames test, thus underscoring their possible carcinogenic potential.