Neoplasms are usually classified according to their histology, location, or the occurrence of specific molecular markers. The development of new technologies has led to the necessity of applying more efficient and universal methods of analysis, enabling a better diagnosis of the type of cancer and the determination of risk groups. Microarray technology constitutes the completion of conventional analytical methods. It shortens the time for a complete and precise characterization of cancer cells. Molecular classification based on microarray technology reflects the biological and clinical variety of neoplastic diseases. Gene expression profiles enable precise diagnosis, scoring and grading, and risk factor stratification. This technique might thus lead to targeted therapy in each type of cancer. This type of strategy has already been used in several types of pediatric cancer, such as leukemia, lymphoma, and sarcoma. In this review the possibilities of a microarray-based classification of pediatric cancers are presented.