The mammalian retina, brain, spinal cord, and peripheral ganglia are all heterogeneous tissues. Each is composed of neuronal and glial cell partners embedded in a connective tissue bed and supplied by vascular and immune cells. This complicated structure presents many challenges to neuroscientists and cell biologists, e.g., how to carry out a quantitative study of neurons in a mature animal surrounded by the hormonal and immune stimuli. A reductionist view leads investigators to study single neurons in vitro, subtracting the immune and vascular components and simplifying the problem. While this has advantages, it limits relevance of the study. We present a method for studying the axonal transport of Herpes simplex virus in mature neurons in situ. Using genetically identical mice and carefully controlling the delivery of virus, an investigator can obtain insight into the transport of virus to and from the neuron cell body within the cellular environment of an intact animal.