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This chapter discusses the basic concepts and methods by which the topological structure of DNA molecules is determined. Knotting and catenation are the true topological properties of DNA molecules. They can only be changed by breakage and reunion of the phosphodiester backbone of DNA, and not by any kind of structural deformation such as condensation or twisting. The two principal methods used for determining the topology of knots and catenanes are agarose gel electrophoresis and electron microscopy. Although only electron microscopy gives the complete stereostructure of individual molecules, electrophoresis provides a more rapid and quantitative overview of the population. It is best, therefore, to use both methods in combination. Gel electrophoresis can resolve even complex mixtures of nicked knots or catenanes into discrete ladders. Traditional techniques for the electron …