Primary CNS tumors (PCNSTs) encompass a broad and heterogeneous group of tumors, including gliomas, meningiomas, embryonal tumors, primary CNS lymphomas, CNS germ cell tumors and sellar region tumors. In recent decades, research has focused on understanding the clinical and biological significance of molecular abnormalities detected in PCNSTs. The emergence of genomic arrays, including comparative genomic hybridization and SNP arrays, have helped in the discovery of novel critically important genes and novel genomic biomarkers involved in PCNST oncogenesis (e.g., BRAF duplication in pilocytic astrocytoma). Since a summary of data from genomic arrays using gliomas has been described in a previous review, in this article we will focus on the insights provided by genome-wide DNA arrays in the genetics and genomics of nonglial PCNSTs in adults. The high-throughput assessment of gene copy-number abnormalities has improved our knowledge of molecular pathogenesis in nonglial PCNSTs, allowing for the identification of new candidate genomic regions and genes involved in tumorigenesis. These chromosome imbalances provide a promising insight into potential targets for innovative drugs and new interesting diagnostic and prognostic biomarkers for clinical practice.