Powerful transneuronal tracing technologies exploit the ability of some neurotropic viruses to travel across neuronal pathways and to function as self-amplifying markers. Two main classes of viral transneuronal tracers are available, derived from alpha-herpesviruses (Herpes Simplex virus type 1, Pseudorabies) and rabies virus. Depending on the virus type and strain, there are major differences with regard to host range, peripheral uptake, replication mechanisms, transport direction and specificity. While alpha-herpesviruses are the tracers of choice for studying autonomic innervation, rabies virus is the ideal tool for studying motor innervation, since its peripheral uptake occurs exclusively at motor endplates. Rabies virus is the only viral tracer that is entirely specific, as it moves exclusively across chemical synapses by strictly unidirectional (retrograde) transneuronal transfer without altering neuronal metabolism, allowing for the stepwise, time-dependent, identification of neuronal networks across an unlimited number of synapses. This review will highlight and contrast the different properties of these viral tracers, and summarize the methodological issues that are critical for the appropriate execution and interpretation of transneuronal tracing studies. Combinations of viral tracing with other methodologies will be evaluated. Emerging technologies, based on genetically modified herpes and rabies tracers, will be also discussed and put in perspective.