Cytogenetic research has had a major impact on the field of medicine, especially in oncology and reproductive medicine, providing an insight into the frequency of chromosomal abnormalities that occur during gametogenesis, embryonic development, and tumor development (1). This is well emphasized by the continuing focus on genetic abnormalities that are associated with, as well as probably responsible for, tumor origin, tumor progression, spontaneous abortions, and congenital anomalies. However, information on recurrent chromosomal aberrations in solid tumors and in some hematological cancer is still limited. The growth of solid tumor in culture for cytogenetic analysis is poor and is compounded by low mitotic indices (2). Often the specimens are contaminated with bacterial and other microbial agents and might contain large regions of necrotic tissue. In addition, the major clone that does grow might not reflect its true representation in the tumor in vivo, where multiple subclones exist with complex chromosomal alterations, making identification of primary genetic changes difficult. Furthermore, solid-Tumor metaphase chromosomes often have poor morphology (1). A newly described molecularcytogenetic technique that does not rely on growth of the tumor in culture might well accelerate the rate at which perturbed chromosomal regions can be cytogenetically identified and molecular-genetically characterized in solid tumors (2). In the past decade, fluorescence in situ hybridization (FISH) has significantly improved the cytogenetic analysis of tumors. FISH uses specific chromosomal probes, usually composed of cloned fragments of DNA (3). These probes will anneal only to their matching complementary DNA sequences on target chromosomes and can accurately detect and target one specific gene or chromosome region at a time. However, the application of FISH in cytogenetic analysis leaves the majority of the genome unexamined (4). Now, these limitations can be circumvented through the use of molecular cytogenetic approaches referred to as new FISH-based technologies, including reverse FISH, multiplex FISH (M-FISH), spectral karyotyping (SKY), comparative genomic hybridization (CGH) analysis, and matrix or microarray-CGH (M-CGH) (4). These technologies have bridged the gap between molecular genetics and conventional cytogenetics. The combination of traditional cytogenetic techniques with moleculargenetic methodologies has added a new and powerful dimension to human genetics. Although the information derived using reverse FISH is highly informative, the procedure is technically demanding and requires specialized micromanipulation equipment to microdissect the region of interest from abnormal chromosomes (3). Among these technologies, CGH has provided an unparalleled insight into the nature of chromosome imbalance in disease development and progression. CGH-based technology is able to discover and map genomic regions for chromosomal gains or losses in a single experiment without any prior information on the chromosomal aberration in question (5). This ability addresses many of the deficiencies of FISH and conventional cytogenetic analyses. CGH produces a map of DNA sequence copy number changes as a function of chromosomal location throughout the entire genome (6). In a typical CGH experiment, genomic DNA from tumor and normal tissue is separately labeled with different fluorochromes (green color for tumor and red for normal control); these differently labeled DNA probes are hybridized simultaneously to metaphase chromosome spreads prepared from normal individuals (7). In addition to different fluorochromes for labeling (in the direct method), haptens (in the indirect method) are also frequently used as labeling dyes because of their flexibility and cost-efficiency. CGH is also performed with differentially labeled normal DNA as a reference standard for data analysis. Detailed analysis is performed using a sensitive monochrome cooled charge-coupled device (CCD) camera and automated image analysis software. Regions of loss or gain of DNA sequences are seen as changes in the ratio of the two fluorescence intensity ratio profiles along the target chromosomes. Thus, gene amplification or chromosomal duplication in the tumor DNA produces an elevated green-To-red ratio, and deletions of chromosomal loss cause a reduced ratio (8-11). This chapter will focus on the technique of CGH and its modifications and will review the genetic perturbations revealed by CGH for a number of tumor types and its potential application in clinical practice.