The maldevelopment of the midline structures is connected with neurologic disorders. The cavum septum pellucidum (CSP) exists in the fetal period, then it is re-absorbed. The presence of unfused leaflets/fornices may be considered important in the genesis of neurodevelopmental abnormalities inclunding epilepsy. The limbic system includes a group of interconnected gray and white matter structures; in this circuit, the fornix is an important white matter connection with the septum pellucidum. Five children, 3-10 years of age, with epilepsy and an unfused septum pellucidum and fornices on MRI, were evaluated by diffusion tensor imaging-fiber tracking (DTI-FT) in order to explore the integrity of the axonal microenviroment of these structures. The patients had generalized tonic-clonic seizures (GTCS). The electroencephalogram (EEG) showed focal-temporal abnormalities with secondary generalization. Magnetic resonance imaging (MRI) and DTI-FT demonstrated the CSP, and the presence of the fornix's body split into two bundles with the fornices separated. The fornix appears more involved than CSP alone, as suggested by fornix atrophy observed in MTLE. Even if epilepsy is suggested to be a grey matter disorder, changes in the underlying brain connectivity have an important contribution in seizure generation and diffusion. In addition, the interconnections of medial septal area with hyppocampus, amygdala and entorhinal cortex, have led to the hypothesis of functional limbic epilepsy. In our patients, the role of DTI was not conclusive since the definition of the number of unmyelinated fibers responsible for epilepsy could not be demonstrated probably for a limited number of seizures and for a short period of drug administration.