Here we investigated the effects of electroacupuncture over the cognitive deficits in the pilocarpine model of epilepsy in rats. Acupuncture stimulation was provided at acupoints located in either the midline of the back and of the head [HD]: Gv-20 (Baihui), Gv-14 (Dazhui), Gv-2 (Yaoshu) and M-HN-3 (Yin Tang); or acupoints located in the limbs [LB]: St-36 (Zusanli) and Sp-6 (Sanyinjiao). In the elevated T-maze test, electroacupuncture at HD and LB acupoints produced an improvement in the acquisition and retention parameters. Retention in the inhibitory avoidance test was seen only in short-term retention and only for animals stimulated at HD. At histology it was found that electroacupuncture at HD acupoints abolished tissue shrinkage in dorsal hippocampus, basolateral nucleus of the amygdala, substantia nigra and perirhinal cortex, whereas stimulation of LB acupoints prevented tissue shrinkage in all of the above structures except dorsal hippocampus. Administration of p-chlorophenylalanine, a serotonergic releaser, abolished both behavioral and part of the histological changes in these animals. We conclude that electroacupuncture at HD and LB acupoints prevents atrophy of some limbic structures and improves cognitive deficits in pilocarpine-epileptic rats and that this effect is dependent on the serotonergic system.