A container for sterilizing flexible bags can be for pharmaceutical use. The container includes an upper flat structure including at least one element supporting the flexible bags and designed to accommodate a plug port of the flexible bag. The support element includes at least one fastening element, which is suitable for retaining the flexible bags once they are inserted into the support element. The container also includes a lower receptacle designed to contain the upper flat structure and to couple to the upper flat structure in a detachable manner. The container further includes a cap for hermetically sealing the lower receptacle.