We describe the case of a baby-girl affected by the Koolen-de Vries syndrome (KdVS), with epilepsy. Our patient has microdeletions in the 17q21.31 region (array CGH). Therapy with Levetiracetam showed a relatively lack of efficacy, while adding a low dose of Topiramate in the therapy allowed the complete seizures control. KdVS is a rare syndrome and its epilepsy features and seizures treatment are not well known by pediatric neurologists. However, with broader use of array CGH, an increasing number of cases are likely to be identified and their description, including response to specific medications, can facilitate recognition and treatment. The complex treatment of epilepsy should be part of the global management and counseling in these composite patients.