BACKGROUND: The majority of the presently known nonrandom chromosome changes in hematologic malignancy were described during the 1970s and 1980s. The last 10 years have been devoted to the location of oncogenes and tumor suppressor genes altered as a consequence of those changes. New molecular methodology has helped speed this process, which has resulted in DNA sequencing of many of the genes involved, permitting molecular detection of abnormal clones. METHODS: This review examines the most common alteration-based subgroups of cytogenetics and molecular genetics in hematologic disorders with the exclusion of lymphoma. Prognosis has been updated to reflect improving treatment protocols. RESULTS: The versatility of cytogenetics for delineating genetic changes is difficult to match by molecular testing. Once a clonal anomaly is identified, molecular methodology can detect residual disease with far greater sensitivity than cytogenetics, but relies on translocation junction targets that exclude clones characterized by deletion or trisomy. CONCLUSIONS: Cytogenetic and molecular testing offers independent diagnostic and prognostic evaluation for most patients with hematologic malignancy.