Previous studies have shown that rats with electrolytic lesions of the nucleus medianus raphe (MR) show alterations in spontaneous alternation and in the acquisition of a delayed spatial alternation task. The current study was designed to investigate whether these changes are secondary to forebrain serotonin depletion or if they are due to the destruction of MR cells or fibers of passage within the region of the MR. To this end, rats were prepared with either an electrolytic lesion of the nucleus, or were given an intra-MR injection of either the serotonin neurotoxin 5,7-dihydroxytryptamine (5,7-DHT) or the excitotoxin ibotenate. Rats were then tested for the presence of spontaneous alternation in a T-maze, and were subsequently also trained on a contingently-reinforced delayed alternation task. Only the group with electrolytic lesions showed significant response perseveration in the spontaneous alternation task, although both the electrolytic and ibotenate groups were impaired in acquiring the delayed alternation task. Rats with 5,7-DHT injections performed comparable to controls in both tasks despite the fact that forebrain serotonin levels in this group were reduced at least as much as in the other two lesioned groups. These results suggest that these behavioral effects of MR lesions are due to the destruction of non-serotonergic fibers and/or cells within the region of the nucleus.