Many fluorescent retrograde tracers are commercially available for neuroanatomical studies. They have been used with varying success in different models and can be very effective in the study of the facial nerve and nucleus. We compare the tracers Fast Blue (FB), Fluoro-ruby, Fluoro-emerald, Fluoro-Gold (FG), and DiI in the rat facial nucleus after application to the buccal division of the nerve. There were no significant differences between counts of cells on the left and right sides of the brain stem with any of the tracers. FB produced a lower sample variation than the other tracers, and together with DiI, demonstrated greater axonal labelling when applied to the surface of the epineurium. FB and FG resulted in strong retrograde labelling of the facial nucleus after only 2 days from injection. All the tracers produced adequate cell labelling after 1 week from nerve application. This labelling persisted for up to 8 weeks for most tracers except FG, which did not produce satisfactory labelling at 8 weeks.