The karyotypic changes in malignant turner cells are unevenly distributed throughout the human genome. Modern cancer cytogenetics showed that different chromosomal bands are preferentially involved in rearrangements in different neoplasms and specific aberrations were identified. Due to the availability of bone marrow cells first insights were done into pathogenesis of hematologic malignancies and were accompanied by elucidation of the role of chromosomal translocations and deletions. Deletions result very often in loss of a tumor suppressor genes whereas specific translocations and inversions lead to the two principal consequences: 1. new fusion gene encoding chimeric protein is created-mostly in myeloid disorders, 2. gene for the immunoglobulin or T-cell receptor is moved near to the proto-oncogene and enhaces its activity - mostly for lymphoid disorders. All three above mentioned rearrangements were later on proved in solid tumors as well. The breakpoints of many translocations specific for different hematologic and solid tumors have been cloned and serve as molecular markers for diagnosis. Cytogenetic analyses are part of the routine workout of the patients. A variety of molecular techniques are now available for wide genome screening of alterations in copy number, structure and expression of genes and DNA sequences. Molecular cytogenetics has special methods: fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), spectral karyotyping (SKY) and multicolor FISH (mFISH). Except for the basic research of human neoplasias all these methods are used routinely to monitor the effect of the treatment and follow the residual tumor cells after chemotherapy and/or bone marrow transplantation.