The invention provides a method for inactivation or reduction of pathogens, microorganisms or parasites in a sample, media, composition, utility, device, surface or organism by treatment with an alkylating compound of Structure I, followed by elimination or reduction of the residual compound with Structure I by treatment with a neutralizing agent, which eliminates or reduces the toxicity or other undesirable properties of the alkylating compound with Structure I. The neutralizing agent may be present in a treatment solution or be part of a solid-phase agent, and preferably acts by eliminating the alkylating properties of the compound of Structure I.