Clinical studies confirm that mental illnesses such as autism, Obsessive Compulsive Disorder (OCD), etc. show behavioral abnormalities even at very young ages; the early diagnosis of which can help steer effective treatments. Most often, the behavior of such at-risk children deviate in very subtle ways from that of a normal child; correct diagnosis of which requires prolonged and continuous monitoring of their activities by a clinician, which is a difficult and time intensive task. As a result, the development of automation tools for assisting in such monitoring activities will be an important step towards effective utilization of the diagnostic resources. In this paper, we approach the problem from a computer vision standpoint, and propose a novel system for the automatic monitoring of the behavior of children in their natural environment through the deployment of multiple non-invasive sensors (cameras and depth sensors). We provide details of our system, together with algorithms for the robust tracking of the activities of the children. Our experiments, conducted in the Shirley G. Moore Laboratory School, demonstrate the effectiveness of our methodology.