Analysis of nucleic acids is playing an increasing role in the diagnosis and management of patients with hematopoietic neoplasms. The tests include those for detection of clonality by analysis of gene rearrangements in the antigen receptor genes or detection of nonrandom inactivation of the X chromosome, detection and quantification of junctions formed by chromosomal translocations, detection of micromutations, quantification of chimerism after allogeneic hematopoietic transplantation, and quantification of normal DNA or RNA sequences. The methods used in clinical molecular hematopathology include end-point PCR, reverse-transcriptase PCR, real-time fluorescence-based PCR, DNA sequencing, FISH, and hybridization-based microarray and microbead assays. Clinical and Laboratory Standards Institute document MM05-A2 - Nucleic Acid Amplification Assays for Molecular Hematopathology; Approved Guideline - Second Edition addresses the needs of the laboratory by providing recommendations on a variety of laboratory tests based on analysis of nucleic acids. It addresses preexamination and examination issues affecting assay performance, reporting of laboratory results, and QA. The guideline is designed to assist a molecular diagnostic laboratory in acquiring a new assay or new technology, as well as serve as a refresher for those already experienced with a particular area of analysis.