A mechanism is provided in a data processing system for de-duplication aware secure delete. Responsive to receiving a secure delete request for a file, the mechanism identifies a list of file blocks to be securely deleted from a physical disk device. Responsive to determining at least one virtual block of another file refers to a given disk block corresponding to a file block in the list, the mechanism copies the given disk block to generate a copied disk block in the physical disk device and updates a pointer of the at least one virtual block to refer to the copied disk block. The mechanism writes a secure delete pattern for each file block in the list of file blocks to a disk block in the physical disk device without performing de-duplication processing.