Over the past decade, utilization of microarray technology has flourished in biomedical research. It has evolved rapidly into a revolutionary tool that offers deeper insight into the molecular basis associated with complex diseases, especially in the field of cancer. Specifically, array-based Comparative Genomic Hybridization (aCGH) permits the detection of genome-wide copy number alterations with high resolution. Microarray application to DNA extracted from formalin-fixed paraffin-embedded tissue (FFPE), in particular, poses a challenge due to the partially degraded nature and compromised quality of the DNA. This chapter gives a description of the several CGH-microarray platforms currently available and offers practical steps that guide you through optimal handling and superior aCGH data acquisition of DNA extracted from FFPE tissues.