Normal functions of the cell are based on the precise regulation of various genes. If this strict regulation and the hierarchy of genes becomes upset due to flaws in this system, the result will be cellular dysfunction which eventually may lead to carcinogenic transformation. Two basic challenges of the classification of cancers are the discovery of new molecular markers characteristic to defined disease groups and the classification of already diagnosed or new cases into existing groups. This precise classification may open the door to tailored treatment or project the expected outcome of the disease. Today there is unlimited access available to the databases containing sequences and localization of the genes within the confines of Human Genome project. It provides significant help for the discovery of chromosome abnormalities and systematic analysis of gene expression patterns. This is important not only to understand normal functions of the cells, but it also contributes to the identification of new genes that are characteristic to given disease groups as markers and that are potential drug targets. Until the second half of the twentieth century the study of the function and regulation of genes was based on step-by-step investigation of individual genes. Regarding the fact, that the genomes of an increasing number of organisms have become known in whole or in part, numerous new techniques have been developed that facilitated the systematic analysis of gene functions. The aim of this study is to summarize the new, molecular based possibilities for classification, diagnosis and prognosis of hematological malignancies, as well as to summarize the main results of these areas.