We investigated the interactions of different types of human and porcine renal proximal tubule-derived cells with core-shell CdSe@ZnS quantum dots (QDs) coated with polymerized histidine-formaldehyde (pHF). The results revealed that porcine and human proximal tubule cells showed a markedly different uptake behavior. This applied to flat epithelial monolayers, as well as to proximal tubules formed on two-dimensional (2D) surfaces in vitro. Primary human cells were most sensitive to the cytotoxic effects of QDs, but displayed inter-donor variability, which appeared to depend on the state of differentiation. The results suggested that human proximal tubule-derived cells were more appropriate than porcine cells for in vitro nanotoxicology. Primary human cells might be suitable when their state of differentiation and inter-donor variability were well-controlled. Furthermore, the results suggested that gel-free proximal tubules formed in vitro could be used as test system to address uptake and transport of nanometer-sized particles in human renal structures.