Comparative genomic hybridization (CGH) can be used in human for comprehensive analysis of chromosomal abnormalities of the entire human genome at low resolution. Genomic DNA from a tested sample (test DNA) and from a normal sample (reference DNA) are labeled differently and hybridized simultaneously to normal metaphase preparations. The ratio of fluorescence intensities along each normal chromosome is analyzed, enabling the detection of regions that are over- or underrepresented in the sample being examined. Even though the higher resolution array-CGH is now widely used instead of CGH in humans, this molecular cytogenetic approach should not be forgotten, as it can also be performed in laboratories equipped only with a three-filter fluorescence microscope. In this chapter, we describe the CGH technique itself and a variant thereof. The so-called micro-CGH technique (= microdissection-based comparative genomic hybridization) enables the molecular cytogenetic analysis of harvested and cytogenetically fixed interphase nuclei. Micro-CGH has already been used in leukemia cytogenetics and clinical genetics.