Pediatric malignancies are a spectrum of biologically diverse cancers different from those seen in adults. Malignant solid tumors diagnosed in children are often, and at least partly the result of developmental pathways dysregulation, and may recapitulate stages of organogenesis. Significant insight into their pathogenesis came from studying normal embryonal and fetal organ development, as well as mechanisms responsible for developmental disorders and congenital syndromes associated with these tumors. Systematic integration of pathology, genetic and molecular analyses of pediatric solid tumors is allowing the recognition of distinct clinical tumor subtypes, as well as potential therapeutic targets for some of these neoplasms. From the diagnostic point of view, some pediatric solid tumors represent examples of clinical translation, as genetic and molecular markers are being incorporated into clinical algorithms, and used for tumor classification, risk stratification, theragnostics or disease monitoring. The on-going comprehensive analysis of some pediatric tumor types using genomic, expression and epigenetic profiling technologies, and the development of experimental tumor model systems, are fastly improving our understanding of their biology. However, further and comprehensive characterization of other pediatric solid tumors, particularly aggressive or chemoresistant cancer types, is still necessary, and should result in the development of new integrated clinical testing, improved therapeutic strategies and better outcomes for these patients.