Acetylcholine receptors (AChRs) are highly concentrated in the postsynaptic membrane at the neuromuscular junction. To investigate mechanisms that lead to the formation or maintenance of this synaptic specialization, we generated transgenic mice in which regulatory elements from the AChR alpha or epsilon-subunit genes are linked to a gene for a reporter protein that is targeted to the nucleus (nlacZ). Both transgenes were selectively expressed and developmentally regulated in muscle; nuclei in both extrafusal (ordinary) and intrafusal (spindle) muscle fibers were labeled. Within individual muscle fibers from epsilon-nlacZ mice, nuclei near synaptic sites were nlacZ-positive, whereas extrasynaptic nuclei were nlacZ-negative. In contrast, nlacZ was expressed in both synaptic and extrasynaptic nuclei when under the control of regulatory elements from the AChR alpha-subunit gene; however, synaptic nuclei were somewhat more intensely stained than extrasynaptic nuclei in a minority of muscle fibers from these mice. Together, our results provide direct evidence for molecular differences between synaptic and extrasynaptic nuclei within a single cytoplasm, and suggest that the motor nerve regulates synapse formation by selectively affecting transcription in synaptic nuclei.