The neuronal damage produced by the mitochondrial toxin 3-nitropropionic acid (3NPA) has been suggested to replicate much of the neuropathology seen in Huntington's disease (HD) and therefore might be used in an animal model. We investigated the susceptibility to this toxin of different neuronal populations in addition to the commonly studied caudate putamen by injecting 3NPA into seven different brain regions as well as systemically. After different survival times, rats were intracardially perfused, brain sections were processed with the Gallyas silver technique, and impregnated neurons were mapped with a computerized microscope. Intracerebral administration of 3NPA resulted in a lesion, the center of which was devoid of tissue while the area was surrounded by a halo of Golgi-like impregnated neurons. In addition to local damage, rats receiving microinjections into the frontal cortex, caudate putamen, basal forebrain, and amygdala displayed argyrophilic neurons in the thalamus corresponding to the topography of thalamofugal neurons projecting to the individual injection sites. On the other hand, negligible secondary damage was seen after injections into the internal capsule, thalamus, or substantia nigra, implicating that thalamofugal axons are especially vulnerable to the local effect of this toxin. Two and a half days after systemic administration of 3NPA, a diffuse argyrophilic neuronal reaction was seen in the dorsolateral part of the caudate putamen, together with a more regionally selective staining of neurons in different cortical areas and the hippocampus. These morphopathological changes were also accompanied by motor deficits. The affected neurons in the cortical regions were primarily in those layers (V and VI) and areas (medial prefrontal, caudal insular/periphinal, and ventral temporal) that do not project toward the lesioned striatal area; therefore, the cortical pathology may represent another primary site of action of the toxin. Among the affected neurons in the hippocampal complex were pyramidal neurons in the CA1 region as well as various neurons in the CA3 region and dentate hilar area. These studies suggest that a combination of 3NPA administration and a sensitive silver-impregnation method may unravel the potential site of primary neuronal damage in this animal model. Furthermore, these findings may contribute to the understanding of how the disease progresses in HD from the originally affected neuronal population(s) by the recruitment of closely related systems and pathways.