Synthetic gene therapy vectors must be designed to safely and efficiently escort DNA from outside the cell to the nucleus and to overcome several physical barriers that are obstacles to internalization, escape from endocytic vesicles, movement through the cytoplasm, and transport into the nucleus. By providing a firm foundation for polymer design, a quantitative understanding of polymer-mediated gene delivery mechanisms may allow more efficient and timely design of new vectors. We have used a flow-cytometry-based assay for investigating endocytic trafficking by quantitation of polyplex pH microenvironments. We investigated polyethylenimine (PEI)- and poly-L-lysine (PLL)-DNA trafficking, with and without the endosomotropic agent chloroquine. PLL-DNA complexes appear to be localized to early endocytic vesicles and are not trafficked to lysosomes. Further, chloroquine appears to facilitate PLL-mediated gene delivery by a mechanism other than buffering of endocytic compartments. Additionally, PEI does not appear to buffer endocytic compartments, but requires exposure to an acidic environment for efficient gene delivery.