Abstract RNA interference (RNAi) is the simplest way of examining gene function by inhibiting expression. However, due to the low rate of introducing short interfering RNA (siRNA) into neurons, it is difficult to discriminate into which neurons that have been successfully introduced. Here, we used neurons from transgenic rats expressing enhanced green fluorescent protein (EGFP), and we simultaneously applied small interfering RNAs (siRNAs) against EGFP and a targeted gene to the EGFP-expressing neurons. EGFP fluorescence and immunoreactivity of the protein were then assessed by immunofluorescence microscopy. Quantitative analysis of the immunofluorescence confirmed that loss of EGFP closely correlates with loss of the target protein. These results indicate that this method can be used in a wider range of the neuroscientific research, especially in genome-wide studies.