Since off-target effects in non-viral siRNA delivery are quite common but not well understood, in this study various polymer-related effects observed in transfection studies were described and their mechanisms of toxicity were investigated. A variety of stably luciferase-expressing cell lines was compared concerning polymer-mediated effects after transfection with polyplexes of siRNA and poly(ethylene imine) (PEI) or poly(ethylene glycol)-grafted PEI (PEG-PEI). Cell viability, LDH release, gene expression profiles of apoptosis-related genes and promoter activation were investigated. Interestingly, PEG-PEI, which is generally better tolerated than PEI, was found to activate apoptosis in a cell line- and concentration-dependent manner. While both polymers showed sigmoidal dose-response of cell viability in L929 cells (IC(50)(PEI) = 6 μg/ml, IC(50)(PEG-PEI) = 11 μg/ml), H1299/Luc cells exhibited biphasic dose-response for PEG-PEI and stronger apoptosis at 2 μg/ml than at 20 μg/ml PEG-PEI, as shown in TUNEL assays. Gene expression profiling confirmed that H1299/Luc cells underwent apoptosis via thousand-fold activation of TNF receptor-associated factors. Additionally, it was demonstrated that NFkB-mediated CMV promoter activation in stably transfected cells can lead to increased target gene levels after transfection instead of siRNA-mediated knockdown. With these results, polymeric vectors were shown not to be inert substances. Therefore, alterations in gene expression caused by the delivery agent must be known to correctly interpret gene-silencing experiments, to understand the mechanisms of off-target effects, and most of all to further develop vectors with reduced side effects. Taking these observations into account, one established cell line was eventually identified to be suitable for RNAi experiments. As shown by these experiments, materials that have been used for many years can elicit unexpected off-target effects. Therefore, non-viral vectors must be screened for several levels of toxicity to make them promising candidates.