The single cell gel electrophoresis or Comet assay is a sensitive, reliable, and rapid method for DNA double- and single-strand breaks and alkali-labile sites, in eukaryotic individual cells. In recent years, this method has been widely used for studies on DNA repair, genetic toxicology, environmental biomonitoring and apoptosis. In this paper, the progress of the assay in: (1) fluorescence in situ hybridization with comet, (2) the use of repair enzymes to detect specific classes of DNA damage, and (3) DNA-specific dye, slide storage and analysis of comet were reviewed.