Engineered nanoparticles are increasingly used in consumer products. While the potential of these products hold great promise, it is not known what potential toxic effects these nanomaterials may have on human health. There is a need to develop affordable, systematic, short-term in vitro assays aimed at allowing rapid assessment of potential toxicity. The method reported in this paper describes a system in which the intestinal lining is mimicked (Caco-2 human intestinal cell line) and provides an environment in which quantum dots (QDs), and possibly other nanomaterials, can be applied. Transepithelial electrical resistance (TEER) measurements assessed whether the epithelial integrity was breached because of QD exposure. QDs were suspended in calcium/magnesium-free phosphate buffered saline to study non-aggregated QDs. To maintain cell integrity, normal cell culture conditions were retained below the epithelium to provide necessary nutrients and ions. Toxicity studies completed here show that the nanosized QDs coated with hydrophilic thioglycolate capping ligands purchased for these experiments caused disruption in the epithelium monolayer and cell death at 0.1mg/L of QDs. This toxicity was caused by the nano-size of the QDs rather than the cadmium ions or the sodium thioglycolate capping ligands. Aggregated QDs did not cause toxicity as measured by TEER.