A file geodatabase is stored as a folder of files on disk, while a personal geodatabase is stored in a single .mdb file. When you first add data to either of these geodatabases, the records within each file are in order and are accessed efficiently by the file system. However, as you delete and add records over time, the records within each file lose their order, and unused space develops as records are removed and new ones are added elsewhere in the file. This causes the file system to perform more record-seeking operations within each file, slowing the rate at which records are accessed.
If you frequently add and delete data, you should compact your file or personal geodatabase on a monthly basis. You should also compact a geodatabase after any large-scale change. Compacting tidies up storage by reordering records and eliminating unused space. After compacting, the data in each file can be accessed more efficiently. Compacting also reduces the size of each file—it's possible to reduce the size of a geodatabase by one-half or more.
In addition to compacting a geodatabase, Windows users should also run the disk defragmenter occasionally to maintain overall file system performance. File and personal geodatabase performance can benefit from this operation just like other types of files can. The disk defragmenter is a tool that comes with the Windows operating system; for more information, see your operating system's online help.
To compact a geodatabase, right-click it in the Catalog tree in ArcMap or ArcCatalog, point to Administration, and click Compact Database.