Slit family of proteins is one of the repulsive axonal guidance cues, and it also plays an important role in neuronal migration and branching through the interaction with roundabout receptors. The function and role of Slit family proteins during peripheral nerve regeneration are still unknown. We examined the expressions of Slits 1-3 mRNAs in the facial nerve nuclei after facial nerve transection by in situ hybridization, using Sprague-Dawley rats. Slit 1 mRNA was weakly expressed in the facial motoneurons, and its expression increased from day 5 to day 28 after transection, with the peak on day 14 after axotomy. Slits 2 and 3 mRNAs were expressed in the motoneurons of the facial nerve before injury, but the expression of Slit 2 mRNA was down-regulated from day 1 to day 7 after axotomy, with the peak on the first day after injury. Slit 3 mRNA expression in the axotomized side remained unchanged throughout the examination period. Slits 1 and 2 mRNA expression returned to the normal level on day 56 postoperatively. The difference in expression pattern of Slit family mRNA in the neurons during peripheral nerve regeneration suggests that it plays a different role in axonal regeneration after axotomy of peripheral nerves.