A storage system includes plural storage apparatuses storing data, and a storage controller which transmits and receives data between an external computer and the plural storage apparatuses, and further controls the plural storage apparatuses. Logical devices each representing a logical storage area are defined on the storage apparatuses. When one logical device is in a state of allocation to the external computer and stores data used by the external computer, and the logical device is deallocated from the external computer, the storage controller performs a processing such as erasing data from the logical device to be deallocated. The processing is performed according to the logical device being deallocated.