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DNA is the most common intracellular target for the action of agents used to treat malignant disease, and it is an essential target for mutagenic agents. The comet or single-cell gel electrophoresis method can detect, either directly or indirectly, a variety of DNA lesions, including single-strand breaks, doublestrand breaks, interstrand cross-links, and damage to the DNA bases. Apoptotic cells can be easily identified because highly fragmented DNA in apoptotic cells migrates efficiently. As few cells are required for this method, fluorescence-activated cell sorting becomes a practical way to provide purified, populations for analysis of DNA damage. Comets can be stained with antibodies against incorporated bromodeoxyuridine (BrdUrd) or against specific DNA adducts. Much of the popularity of the comet assay is due to the ability of this method to measure DNA damage in virtually any single cell. A more unique aspect of this method is the ability to detect heterogeneity in response within different cells of a single population. Under alkaline conditions, the comet assay detects DNA single-strand breaks, double-strand breaks, and alkali labile lesions.