Neuroblastoma (NB) is one of the most common pediatric solid tumors and displays a broad variety of genomic alterations. Array-based comparative genomic hybridization (A-CGH) is a novel technology enabling the high-resolution detection of DNA copy number aberrations. In this article, we outline features of this new technology and approaches of data analysis. We focus on stage specific DNA copy number variations in neuroblastoma detected by cDNA array-based comparative genomic hybridization (A-CGH). We also discuss hypothetic evolutionary models of neuroblastoma progression that can be derived from A-CGH data.