A method and apparatus provide for automatically cleaning and decontaminating medical instruments. The method comprising the steps of: a) placing the medical instruments into a container after their use in a medical procedure; b) closing the container to seal the instruments inside whereby to prevent personnel contact with the instruments and any contaminants which might be thereon; c) inserting the sealed container into a washer/decontaminator and sealing the washer/decontaminator; d) the washer/decontaminator automatically opening the container and applying a washing fluid thereto to wash the instruments within the container; and e) the washer/decontaminator automatically applying a disinfectant to the container to disinfect the instruments whereby to allow safe handling thereof by personnel.