DNA is a negatively charged biopolymer composed of monomeric nucleotides each carrying on average a net (-1) charge concentrated in the region of the phosphate backbone. In solution, the net negative charge of the molecule is presumably balanced by positively charged cations that interact with the DNA. Important questions arise as to the molecular details of the interaction of different cations with DNA. In this paper, we investigate the interaction of monovalent sodium ions and divalent magnesium and calcium ions with duplex DNA using molecular dynamics. Three 50 ps molecular dynamics simulations of the DNA sequence d[CGCGAATTCGCG]2 have been performed in different ionic environments. Each system is constructed to be electrically neutral and is composed of the DNA duplex immersed in a large water bath containing a specific ionic species [Na(I), Mg(II), or Ca(II)]. The structural differences of the DNA itself as a result of interacting with each ionic species have been previously examined (D. M. York, T. Darden, D. Deerfield, II, and L. Pedersen, J. Biomol. Struct. Dyn., submitted). In the current work, the ion–DNA and ion–water interactions are examined. The coordination shells of the ions and distributions around the phosphate anions are reported, and both show close encouraging agreement with available experimental work. The results of our studies indicate that the hydration state of the ion plays an important role in the direct coordination of the phosphate anions. Na(I) and Ca(II) ions prefer to coordinate the phosphate anions directly, whereas Mg(II) ions have a greater tendency to interact with phosphate anions as fully hydrated cations.