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Dorsal root ganglia (DRG) are comprised of soma from afferent neurons innervating various parts of the body, and important insights can be gained from studying sensory neurons with different innervation targets1. Various indirect or invasive methods are used to isolate and identify afferent neurons for e.g. injecting the nerve with markers like fluorogold1, injecting dye into the muscles by surgical method2. Of the different dyes that have been successfully used to label neurons and neuronal tracts, fluorescent dyes like DiI are widely used in neuroanatomical tracings owing to their rapid uptake by neuron terminals, long term retention in neurons, and the lack of transfer between neurons3. The afferent neurons labeled with DiI can be easily visualized using a fluorescent microscope for detailed study. However, one limitation is that markers such as DiI can be lost from cells during cell permeabilization needed for immunocytochemistry with intracellular epitopes4. Here we describe a method that uses DiI injected into skeletal muscle to identify muscle afferent neurons in the DRG. We also describe a cell permeabilization method that retains DiI in the neuron while permitting antibody access to intracellular epitopes. We demonstrate use of both patch clamp electrophysiology and immunocytochemistry to study these identified neurons, as well as describe the distinct advantages of each technique in studying ion channels that control neuronal excitability. Finally, we describe potential problems that can hinder interpretation of electrophysiological data. We have used these methods to identify muscle and cutaneous afferent neurons and determine the voltage-gated sodium (NaV) channels expressed in these identified neurons8. However, these methods can be adapted to a variety of preparations for studying identified subsets of neurons innervating a particular target tissue or brain nucleus.