A method of treating the surfaces of medical instruments which are contaminated with prions includes contacting the surface with a composition containing a source of peroxide ions, such as hydrogen peroxide, at a molar concentration of at least 1.5M peroxide (equivalent to approximately 5% hydrogen peroxide) and preferably, about 2M peroxide (approximately 7% hydrogen peroxide). The composition is optionally in the form of a gel. The composition is retained in contact with the surfaces for about 1-2 hours until all or substantially all prion contamination is removed.