Neural manipulations were used to examine the mechanisms that underlie the acquired equivalence and distinctiveness of cues in rats. Control rats and those with excitotoxic lesions of either the hippocampus (HPC) or entorhinal cortex (EC) acquired the following conditional discrimination: In Contexts A and B, Stimulus X-->food and Stimulus Y-->no food, and in Contexts C and D, Y-->food and X-->no food. Rats then received many food pellets in A but not in C. After this treatment, control rats showed more magazine activity in B than in D--an acquired equivalence-distinctiveness effect. This effect was also evident in HPC rats but not in EC rats. These results indicate that changes in stimulus distinctiveness are dissociable from the process of conditional learning.