In the growth of endotaxial nickel disilicide on Si(001) using reactive deposition epitaxy, three types of structures, which include the inverted-hut structure containing only the A-type NiSi2/Si interfaces, the parallel-epipedal structure, and the nanowire structure containing the B-type NiSi2/Si interfaces, can be observed. In this paper, we show that the formation of both the nanowires and the parallel-epipedal structures is related to the substrate surface-cleaning process and deposition temperatures. The formation of both the nanowires and the parallel-epipedal structures can be suppressed either with the high surface-cleaning temperature or at the low Ni deposition temperature. (C) 2008 The Electrochemical Society. [DOI: 10.1149/1.3058995] All rights reserved.