In the past decade, the literature describing how viruses can be used to define the synaptic architecture of the brain has increased dramatically. Early studies focused on determining the specificity of viral transport through synaptic connections. Analysis of the assembly and intracellular transport of viruses as well as of the role of the brain response to infection were central to this literature. With the growing acceptance that the transport of viruses is circuit-related, attention has shifted to application of the method to define the functional architecture of neural systems. The development of attenuated recombinant viruses that maintain neuroinvasiveness has been instrumental to the generation of increasingly powerful experimental approaches for the functional dissection of neural circuits. These approaches include the use of recombinant viruses that express unique reporters to address issues of axon collateralization in complex circuits, the use of green-fluorescent-protein-expressing recombinants to characterize the electrophysiological properties of projection-specific neurons in live slices of brain, and the exploitation of the Cre recombinase system for conditional replication of virus in phenotypically defined populations of neurons.