Before the recent advances in molecular biology and the knowledge of the complete nucleotide sequence of several genomes, cytogenetic analysis provided the first information concerning the genome organization. The most important contribution of cytogenetics is related to the physical anchorage of genetic linkage maps in the chromosomes through the hybridization of DNA markers onto chromosomes. Cytogenetic approaches to studying chromosomes and their relationship to human disease have improved greatly over the past several decades. The cytogenetic mapping techniques of fluorescence in situ hybridization (FISH), which enables the direct chromosomal localization of labelled DNA probes and Comparative genomic hybridisation (CGH) is a technique that permits the detection of chromosomal copy number changes without the need for cell culturing. It provides a global overview of chromosomal gains and losses throughout the whole genome of a tumour. Another cytogenetic technique used to isolate populations of intact cells involved the process known as flow Cytometry which uses the fluorescent dye to label the cell population of interest. Practical applications of these techniques in genome analysis, chromosome mapping, analysis of somaclonal variations in tissue culture and many more have been presented.