Both reinnervated and dormant neurons can be observed in facial nucleus following facial-facial anastomosis. Although they may play different roles in the remodeling mechanism of facial nucleus during facial nerve injury and regeneration, comprehensive gene profiling analysis of these two neuron types has never been performed due to the difficulty in isolating specific neuron populations and extracting sufficient amount of RNAs from the heterogeneous facial nucleus. In this study, we developed a method to isolate the Fluoro-Ruby (FR) retrogradely labeled reinnervated facial motor neurons and the Nissl stained dormant neurons in two steps with laser capture microdissection (LCM) technology. The quality and yield of RNAs extracted from these isolated neurons were confirmed with Agilent 2100 Bioanalyzer. This modified LCM based neuron isolation method will facilitate the studies of the roles and interactions of different neurons that co-exist in the same facial nucleus after peripheral injury. (C) 2009 Elsevier Ireland Ltd. All rights reserved.