A method for decontaminating a medical instrument having parts that are movable relative to one another involves mounting the instrument in a decontaminating apparatus, and automatically manipulating the instrument to provide relative movement between two or more relatively movable parts of the instrument during an automated decontamination cycle of the decontaminating apparatus. The instrument may be a surgical instrument having an operating portion arranged to remotely control operation of a working portion in use. The method may involve engaging a part or parts of the operating portion to transmit motion thereto for creating the relative movement. An instrument carrier insertable in a decontaminating apparatus in use may be modified to incorporate an instrument manipulator.
