Spatial alternation performance in rats is usually evaluated with the T-Maze. The first aim of this study was to analyze the effect of a selective lesion of medial prefrontal cortex (mPFC) on performance in a T-maze. Second, we wanted to validate a new test using alternation in a water maze (AWM). The mPFC of 21 male Sprague-Dawley rats was lesioned bilaterally using in situ microinjection of ibotenic acid. Thirteen control rats received injections of the vehicle only. Results show that mPFC lesioned rats were significantly impaired in the T-Maze as well as in the AWM compared to controls. These results validate the AWM as a frontal cortex dependent task probing working memory and/or behavioral flexibility. We suggest that the AWM may be more powerful than the T-maze as an investigational tool, given that is can be easily compared to other water maze tasks that evaluate other (nonfrontal) cognitive modules.