Background: The tumors of the central nervous system (CNS) are the first cause of cancer death among children and have high fatality rates also among adults. Accurate diagnosis, necessary to guide treatment decisions, is often challenging due to high heterogeneity and particular location of these tumors. However, molecular markers have been revolutionizing the field, providing tools for precise diagnosis, which may give rise to more effective treatments. Methods: In this chapter, we present a narrative review, based on the analysis of various guidelines and recommendations for diagnosing CNS tumors as well as other scientific publications on the topic. Results: It was not our ambition to provide a comprehensive list of all currently recognized diagnostic molecular markers. We show how the development of molecular biology techniques is changing cancer diagnosis and how molecular biomarkers are becoming an inherent part of the diagnostic workup. This is backed up by practical examples that illustrate these changing concepts. We also provide some predictions as to future trends and new perspectives in this important and fascinating field. Conclusions: Molecular markers are indispensable tools for diagnosing CNS tumors. Adding molecular analyses to classic pathologic analysis of histologic slides has resulted in an integrated morphological and molecular CNS diagnosis system, with significant clinical implications.