Halogens in aqueous solution are still used world-wide as disinfectants. During the process of halogenation, the substances present in water undergo several chemical processes, yielding relatively unstable intermediate species; their life-times in the medium depend on their structure and on the physico-chemical conditions. Several low molecular weight hydrocarbons are formed during water halogenation, some of them potent mutagens and/or carcinogens. Halogenation also takes place in vivo involving the system myeloperoxidase/H₂O₂/halide, which increases the relevance of such reactions and opens new research fields.