In adult rats, each neuromuscular compartment of the lateral gastrocnemius muscle (LG) is exclusively innervated by a primary branch of the LG nerve. In neonates, however, a small percentage of LG cells receives inputs from more than one primary nerve branch; these inputs are known as cross-compartmental. Cross-compartmental inputs are normally lost from the medial compartment of LG (LGm) by the 8th postnatal day. To investigate the mechanisms involved in the elimination of cross-compartmental inputs, muscle fibers in the LGm compartment were denervated by cutting the LGm nerve branch in 1-4 day old rat pups and in adult rats. We then assessed the degree of cross-compartmental innervation within the "denervated" compartment using intracellular recordings from neonatal muscle fibers or immunohistochemical staining for nerve cell adhesion molecule (N-CAM) and neurofilament protein in adult muscles. Following LGm axotomy in neonates, cross-compartmental innervation is more extensive than in controls and is present as late as 20 days after birth. Thus, in the absence of "native" LGm axons, neonatal cross-compartmental inputs proliferate by axonal sprouting and the formation of new synapses on vacant LGm fibers. In contrast, axotomized adults do not form new cross-compartmental inputs over the same time period. The differential response of neonates and adults to muscle nerve branch denervation is evidence for the existence of some form of compartment-specific recognition. We propose that compartmental identity either arises or becomes relatively more potent during ontogeny and normally acts selectively to eliminate foreign axons and deter the formation of new cross-compartmental inputs.