Fenton's reagent (i.e., Fe[II]/H2O2) is known to generate strong oxidants capable of oxidizing a broad spectrum of organic compounds in aqueous solution. This study demonstrates the successful inactivation of MS2 coliphage (MS2) by the oxidants produced from Fenton's reagent. The inactivation process of MS2 by Fenton's reagent was found to proceed in two distinct stages. The first stage inactivation, which took place rapidly within 1 min reaction time, was mainly achieved by the reaction of Fe(II) with H2O2 (i.e., the Fenton reaction). The second stage, which occurred by the catalytic reactions of Fe(III) with H2O2, exhibited much slower inactivation than the first stage. The rate of MS2 inactivation increased as pH decreased from 8.0 to 6.0. The addition of oxalate and humic acids significantly inhibited the MS2 inactivation, whereas 1,10-phenanthroline and bipyridine resulted in a gradual and steady inactivation of MS2. These observations on the effects of pH and iron-chelating agents indicate that oxidants formed on the surface or inside MS2 are responsible for the inactivation.