Although currently no medication has been approved to treat autism spectrum disorders, survey data show that community practitioners are prescribing a broad range of medication treatments, including, but not limited to, antidepressants, stimulants, antipsychotics, alpha agonists, and anticonvulsants. Patients with autism spectrum disorders are also taking alternative treatments, including herbal remedies, immunologic treatments, and vitamin therapies, which may themselves produce side effects and/or create drug interactions with traditional medications. Although short-term data on the efficacy and safety of commonly prescribed treatments for autism spectrum disorders are increasing, few data are currently available on long-term treatment for autism spectrum disorders, but available studies and clinical experience can offer preliminary recommendations on the safety of and monitoring needs for the medications currently used for these disorders. Monitoring the safety and tolerability of drugs used in patients with these disorders should minimize the burden of side effects and optimize treatment outcome.