Ibotenic acid (IBO) or quisqualic acid (QUIS) was infused into the region of the nucleus basalis magnocellularis (NBm) in F344 rats in order to behaviorally and biochemically characterize the effects of these two neurotoxins. QUIS infusion resulted in a slightly higher depletion of choline acetyltransferase (ChAT) activity in both anterior and posterior regions of cortex than did lesions caused by infusion of IBO. Both QUIS- and IBO-treated rats demonstrated significantly longer latencies than controls to find a hidden platform in a Morris water maze task. In addition, QUIS-treated rats performed significantly better than IBO-treated rats in the water maze. Analysis of swim speed and open field behavior did not show significant differences in general motor activity. Passive avoidance retention was unaffected by either neurotoxin. Cortical amino acid levels, [3H]neurotensin binding, dopamine, norepinephrine, and serotonin levels were unaffected by either neurotoxin. The levels of HVA and 5-HIAA in the IBO and QUIS groups were significantly reduced compared to controls, but were not significantly different from each other. Histological examination showed greater damage to non-NBm structures with IBO than with QUIS, including the basolateral nucleus of the amygdala and the reticular formation of the thalamus. The greater behavioral deficit seen after IBO lesions may be due to damage to other areas rather than differences in the extent of depletion of corticai ChAT, amino acids, catecholamines or indolamines.