Motor axons regenerating after transection of mixed nerve preferentially reinnervate distal motor branches and/or muscle, a process termed “preferential motor reinnervation.” Collaterals of a single motor axon often enter both sensory and motor Schwann cell tubes of the distal stump; specificity is generated by pruning collaterals from sensory pathways while maintaining those in motor pathways. Previous experiments in the rat femoral nerve model evaluated reinnervation of the femoral motor branch and quadriceps muscle as a unit. In this study, pathway contributions are analyzed separately by denying muscle contact, or by reinnervating muscle through inappropriate, formerly sensory pathways. Motor axons preferentially reinnervate motor pathways, even when these pathways end blindly in a silicon tube. If the femoral nerve is removed as a graft and reinserted with correct or reversed alignment of the sensory and motor branches, more motoneurons reinnervate muscle through correct motor than through incorrect sensory pathways. Motor pathways thus differ from sensory pathways in ways that survive Wallerian degeneration and transplantation as a graft, and that can be used by regenerating motor axons as a basis for collateral pruning and specificity generation.