Efficient and long-lasting transfection of primary neurons is an essential tool to address many questions in current neuroscience using functional gene analysis. Neurons are sensitive to cytotoxicity and difficult to transfect with most methods. We provide a protocol for transfection of cDNA and RNA interference (shRNA) vectors, using magnetofection, into rat hippocampal neurons (E18/19) cultured for several hours to 21 days in vitro. This protocol even allows for double-transfection of DNA into a small subpopulation of hippocampal neurons (GABAergic interneurons), as well as achieving long-lasting expression of DNA and shRNA constructs without interfering with neuronal differentiation. The protocol, which uses inexpensive equipment and reagents, takes 1 h, utilizes mixed hippocampal cultures, a transfection reagent, CombiMag and a magnetic plate, shows low toxicity and is suited for single cell analysis. Modifications as done by our three laboratories are detailed.