Thin Au films (∼2nm) were deposited on an Si(110) substrate epitaxially under ultra-high vacuum (UHV) conditions in a molecular beam epitaxy (MBE) system. Real-time in situ transmission electron microscopy (TEM) measurements were carried out at various temperatures (from room temperature to 700°C), which shows the formation and growth of aligned gold silicide nanorod-like structures. The real-time selected-area electron diffraction patterns show the presence of silicon and unreacted gold at lower temperatures (up to 363°C), while at higher temperatures only the signature of silicon has been observed. The diffraction analysis from room temperature cooled systems show the presence of gold silicide structures. Around 700 °C, 97% of the nanostructures were found to be aligned nanosilicide-rod-like structures with a longer side of ≈37nm and aspect ratio of 1.38. For a high temperature annealed system (at 600 °C), selected-area diffraction (SAD) and high resolution lattice (after cooling down to room temperature) confirmed the formation of nano- Au 5Si2 structures. The alignment of gold silicide structures has been explained on the basis of lattice matching between the substrate silicon and silicide structures. © 2009 IOP Publishing Ltd.