Injections of the neurotoxin kainic acid were made unilaterally at multiple loci in the cerebral cortex of the rat in an attempt to reproduce aspects of the central pathology of Alzheimer's disease. Neurochemical markers of cholinergic and GABAergic function in the cortex and basal forebrain, determined after various intervals, suggested that subsequent to initial destruction of cortical neuronal cell bodies, trans-synaptic retrograde degeneration of cholinergic neurons occurred in the nucleus basalis magnocellularis (NBM) projecting to the cortex. Contrary to the situation noted after devascularizing cortical lesions, there was no spontaneous recovery from this effect of kainic acid in the ipsilateral NBM. Similarly, these retrograde effects could not be prevented by the administration of the ganglioside GM(1). These observations suggest that kainic acid compromises the plastic capacity of this cholinergic projection, perhaps by affecting the production of endogenous trophic factors. This may be of relevance in developing the use of neurotoxins for models of neurodegenerative disease.