The development of new drugs for the treatment of childhood cancer presents novel challenges, and pediatric clinical trials of a new agent are often initiated many years after testing in adults. It is estimated that there are over 400 new entities being developed as cancer treatments, although few of these have been developed specifically for the treatment of childhood malignancies. This raises the question of how agents can be prioritized for pediatric clinical testing. In this review, the molecular characteristics of childhood cancers that may be valuable in steering choices for rational or molecularly targeted treatments are described, and the Pediatric Preclinical Testing Program, a National Cancer Institute initiative to identify agents that should be prioritized for clinical evaluation against childhood cancer, is presented.