Container for sterilising flexible bags for pharmaceutical use, characterised in that it comprises:a) an upper flat structure comprising at least one element supporting said flexible bags designed to accommodate the plug port of said flexible bag, said support element comprising at least one fastening element, suitable for retaining said flexible bags once they are inserted into said support element;b) a lower receptacle designed to contain said upper flat structure (a) and to couple thereto in a detachable manner; andc) a cap for hermetically sealing said lower receptacle.