Vacancy clusters in graphite have been investigated using Density Functional T heory (DFT) within B3LYP exchange-functional. The smallest size of vacancy clusters (V4) has been chosen to study the migration energy and aggregation mechanism. Two main types of V4 vacancy clusters have been modeled, the disc (V4d) and the line vacancy clusters; including boat vacancy (V4b) and zig-zag vacancy (V4z). The results show that the presence of unst able V3 vacancy may induce the mono-vacancy to migrate with low energy and vanish through forming stable V4 vacancy cluster. Also, the calculated energy barriers required to form the boat vacancy cluster (V4b), the zig-zag vacancy cluster (V4z) and disk vacancy cluster (V4d) support that the disc and the boat vacancy clusters co-exist. However the zig-zag type might only exist by knocking-out mechanism for highly irradiated graphite.