Innovative hypothesis-driven clinical trials have achieved major successes over the past several decades in treating children and adolescents with cancer. DNA-damaging cytotoxic agents have cured children with cancer. While the mission is not yet accomplished, chemotherapy has been validated. None of these drugs were designed specifically for a pediatric disease. Continued progress will require new strategies. Now being tested for adult cancers, these strategies include gene therapy, immunotherapy, cancer prevention, and signal transduction inhibitor (STI) therapy. Of these, the most promising is STI therapy, also known as molecular therapeutics or targeted therapy. For this therapy to succeed, components of signal transduction (i.e., candidate drug targets) must be identified, the targets relevant to cancers, and the drugs available for trial. Because STI therapy is biologically driven and because therapy will be tailored depending on the molecular profile of a specific patient's tumor, clinical pediatric oncologists will need to acquire greater understanding of signaling pathways and their therapeutic relevance. With examples drawn from pediatric oncology, the critical steps in the pre-clinical development of targeted therapy are reviewed here. © 2005 Wiley-Liss, Inc.