Herpes simplex virus infects both epithelial cells and neuronal cells of the human host. Although HSV assembly has been studied extensively in cultured epithelial and neuronal cells, cultured neurons are biochemically, physiologically and anatomically significantly different than mature neurons in vivo. Therefore, it is imperative that viral maturation and assembly be studied in vivo. To study viral assembly in vivo, we have inoculated wild-type and replication-defective viruses into the posterior chamber of mouse eyes and followed infection in retinal ganglion cell bodies and axons. We used PCR techniques to detect viral DNA and RNA and EM immunohistochemistry and western blotting to detect viral proteins in specific portions of the optic tract. This approach has shown that viral DNA replication is necessary for viral DNA movement into axons. Movement of viral DNA along ganglion cell axons occurs within capsid-like structures at the speed of fast axonal transport. These studies show the combined use of intravitreal injections of replication-defective viruses and molecular probes allow the genetic analysis of essential viral replication and maturation processes in neurons in vivo. They also provide novel direct evidence for the axonal transport of viral DNA and support for the subassembly hypothesis of viral maturation in situ.