Here, we present a protocol for staining murine skin innervation by either a pan-axonal marker or a genetic tracer of sensory neuron subtypes using floating sections. We also describe steps for using a new MATLAB-based semiautomated routine that facilitates the quantification of innervation density. This protocol can also be applied to other organs, such as the mouse's spinal cord and tongue. For complete details on the use and execution of this protocol, please refer to Dey et al. 1 .