Chlorine dioxide is a hypochlorite alternative disinfectant agent. In this context, we have determined the products formed in the reaction of ClO(2) with selected amino acids as model compounds that can be present in natural waters. The reaction of tryptophane, histidine and tyrosine (10 ppm each) with ClO(2) were studied at molar ratios ranging from 0.25 to 4 in the presence or absence of oxygen. It was found that in the absence of oxygen adding substoichiometric amounts of ClO(2) creates products that are structurally similar to the starting amino acids. Through a series of cascade reactions the initial product distribution gradually evolves toward simple, small carbon chain products that are far from the starting amino acid. The reaction product distribution revealed that chlorine dioxide can attack the electron-rich aromatic moieties as well as the nitrogen atom lone electron pair. Our study is relevant to gain knowledge on the reaction mechanism of ClO(2) with ubiquitous amino acids present in natural waters.