The structure of epitaxially grown Ni silicide on Si(001) has been studied by scanning tunneling microscopy. Atomically resolved STM images of this surface show unreconstructed (1x1) NiS2 islands and a (2X1) adsorbed Ni layer. The NiSi2 islands often contain twin boundaries with inverse pyramidal structures and "facet bars" at increased coverage. From observed images, it is suggested that the poor reproducibility in the Schottky barrier height of this interface originates from the complex interface structure.