The spectrum of pediatric tumors varies considerably, from those derived from blastemal cells in various organ systems to proliferations of soft tissue supporting cells to hamartomatous processes that mimic malignant tumors. Small round cell tumors are often undifferentiated or poorly differentiated, making it difficult sometimes to provide a definitive diagnosis. Both benign and malignant tumors require a coordinated method for diagnosis, and need a comprehensive evaluation to provide the most appropriate diagnosis for designing therapy and predicting prognosis. Pediatric tumors require the integration of routine histopathologic examination with histochemical, immunocytochemical, ultrastructural, cytogenetic, and diagnostic molecular pathology techniques. This review provides updated guidelines with respect to the application of these special techniques in this rapidly evolving diagnostic arena.