Background: In this study eugenol (EU) loaded nanoemulsions (NEs) emulsified with modified starch were prepared and their apoptotic potential against liver and colon cancer cells was examined in comparison with bulk EU. Materials and Methods: We prepared stable EU loaded NEs whcih were characterized by dynamic light scattering, centrifugation and gas chromatography. Furthermore, cell viability was determined using MTT assay, and apoptosis and cell cycle analysess by flow cytometry. Results: HB8065 (liver) and HTB37 (colon) cells when treated with EU:CA NEs demonstrated greater apoptotic cells percentages as evidenced by microscopic images and flow cytometric evaluations. It was observed that EU and EU:CA NE induced apoptosis in both cell lines via reactive oxygen species (ROS) generation. Conclusions: The present study demonstrated that ROS plays a critical role in EU and EU:CA NE induced apoptosis in HB8065 and HTB37 cells. This is the first report on the antiproliferative mechanisms of EU loaded NE.