In the present study, herpes simplex virus type 1 (HSV1) was injected into the olfactory bulb of the rat in order to determine the impact of viral infection on neural pathways, neurotransmitters, and behavior. In many animals, these injections caused considerable neuronal loss in regions that project to the bulb including the primary olfactory cortex and locus coeruleus (LC). Short-term (2-5 days postinjection) studies using immunocytochemical colocalization of virus and transmitter markers showed that cholinergic (ACh) neurons in the horizontal nucleus of the diagonal band, serotonergic (5-HT) neurons in the dorsal and median raphe nuclei, and noradrenergic (NE) neurons in the LC became infected with virus. Almost all NE neurons in the ipsilateral LC were infected while a smaller proportion of 5-HT and ACh neurons in their respective nuclei contained virus. In order to determine long-term effects of viral infection, virus injection into the olfactory bulb was followed by antiviral treatment and sacrifice 17 days to 7 months postinjection. Quantitative analysis of selected cortical regions (olfactory bulb, cingulate cortex, parietal cortex) revealed decreased NE-immunoreactive fibers while 5-HT axons from the dorsal and median raphe nuclei were not significantly affected. No changes in acetylcholinesterase staining in these cortical regions were observed, indicating that cholinergic axons were not significantly changed. Ten of the 36 animals that survived long-term after HSV1 inoculation were also tested in a water maze task before sacrifice to determine if the viral infection was associated with spatial learning deficits. Spatial learning deficits correlated with the degree of primary olfactory cortex damage but not with 5-HT, NE, or ACh axon losses.