Although cure rates for children with cancer are approximately 70%, improvements in cure rates have slowed in the past decade, likely due to our inability to further improve outcome using currently available drugs. Novel drug approaches are needed for children with difficult-to-treat malignancies, such as stage IV neuroblastoma, sarcomas, brain tumors, and relapsed leukemia. Several novel agents show promise for improving outcome in patients with either high risk or recurrent disease. For leukemia, inhibitors of cell cycle progression, such as clofarabine and nelarabine, have shown great promise in their ability to increase treatment efficacy in high-risk disease. Targeted agents such as tyrosine kinase inhibitors, DNA binding compounds (trabectedin), and monoclonal antibodies (GD2 inhibitors for neuroblastoma and anti-CD22 antibodies for pre-B acute lymphocytic leukemia (ALL)) also show promise for future treatment. Extensive reviews of each of these agents are presented elsewhere; this article provides an overview of molecular agents at different stages of FDA/EMA approval; those that are currently approved for use in children, currently approved for use in adults, as well as those that show promise in early clinical trial testing, or are supported by strong preclinical data.