Method and system for incremental backup of data containers with fixed length records is provided. Initially, a backup application copies all stored data containers to create an initial backup container. A data structure corresponding to the first backup operation is also created. The data structure maintains unique file identifiers for each data container and information regarding when a record was added. The data structure is created and maintained by an application that also creates, updates, and modifies the fixed length records. The application updates the base data structure when records are added to a data container, after the initial backup. For a next backup operation, the initial data structure is compared to an updated data structure that is current at the next backup time. The comparison identifies the new records that were added (or updated) since the initial backup operation. The backup application then incrementally copies the new records.