Spatial segregation of membrane proteins is a feature of many excitable cells. In skeletal muscle, clusters of acetylcholine receptors (AChRs) and voltage-gated sodium channels (Na V 1s) occupy distinct domains at the neuromuscular junction (NMJ). We used quantitative immunolabeling of developing rat soleus muscles to study the mechanism of ion channel segregation and Na V 1 clustering at NMJs. When Na V 1s can first be detected, at birth, they already occupy a postsynaptic domain that is distinct from that occupied by AChRs. At this time, Na V 1s are expressed only in a diffuse area that extends 50 -100 m from the immature NMJ. However, in the region of the high-density AChR cluster at NMJ itself, Na V 1s are actually present in lower density than in the immediately surrounding membrane. These distinctive features of the Na V 1 distribution at birth are closely correlated with the distribution of ankyrinG immunolabeling. This suggests that an interaction with ankyrinG plays a role in the initial segregation of Na V 1s from AChRs. Both Na V 1 and ankyrinG become clustered at the NMJ itself 1-2 weeks after birth, coincident with the formation of postsynaptic folds. Syntrophin immunolabeling codistributes with AChRs and never resembles that for Na V 1 or ankyrinG. Therefore, syntrophin is unlikely to play an important part in the initial accumulation of Na V 1 at the NMJ. These findings suggest that the segregation of Na V 1 from AChRs begins early in NMJ formation and occurs as a result of the physical exclusion of Na V 1 and ankyrinG from the region of nerve-muscle contact rather than by a process of active clustering.