Pharmacotherapy is a frequently employed treatment option in the area of autism spectrum disorders (ASD). A considerable literature base has developed indicating when these medications should or could be administered. However, research on the potential side effects and cost benefit analysis of these treatments is not well understood at this time. The purpose of this review is to assess current prescription practices, to determine what is needed with respect to better understanding the cost and benefits of these prescription practices, and notions about future trends in research to better aid in our understanding of psychotropic drug side effects. Future research of this sort should further establish best practices with respect to pharmacotherapy and ASD.