The study of amyloidogenic beta-amyloid precursor protein (AbetaPP) metabolism and amyloid beta protein (Abeta) production has been a major focus of Alzheimer's disease (AD) neuropathogenesis research. Cell transfection is a commonly employed method for assessing the effects of various genes on AbetaPP processing and Abeta production. Certain cell transfection reagents utilize lipid-based formulations that could potentially affect AbetaPP processing and Abeta production. Thus, we set out to assess the effects of cell transfection reagents with lipid formulations (TKO, FuGene6, RNAifect) on AbetaPP processing and Abeta level in H4 human neuroglioma cells overexpressing human AbetaPP. We found both TKO and RNAifect increase the protein levels of AbetaPP-C-terminal fragments (CTFs) and Abeta levels, while FuGene6 increases the protein levels of AbetaPP-CTFs without altering Abeta level. In contrast, electroporation-based cell transfection does not affect AbetaPP processing and Abeta production in our studies. These results suggest for the first time that lipid-based cell transfection reagents may artefactually affect AbetaPP processing and Abeta production, thereby confounding studies aimed at assessing the effects of transfected genes on AbetaPP metabolism.