Single cell gel electrophoresis (SCGE or comet) assay allows quantification of DNA damage in individual cells and is an ideal tool for use within biological monitoring programmes. Comet assay can be used on a range of cell types including somatic, reproductive (gametes) or circulatory cells in many different species including both marine bivalves and flatfish. The assay can be employed with simple equipment available in most laboratories, is sensitive to environmentally relevant levels of DNA damage (Frenzilli and Lyons, 2009), accurately demonstrates a linear dose response to exposure (Collins et al., 1996), and can be adapted for use on most nucleated cell types. This document concentrates on the simplest and most repeatable method of comet assay in circulatory cells of species commonly used in marine biomonitoring programmes both for chemical and biological effects. This manuscript describes standardized assay procedures and recommends the minimum level of information required when reporting comet assay results