We report on the phase separation in Au-Ge system leading to the formation of lobe-lobe (bi-lobed) Au-Ge nanostructures under ultra high vacuum (UHV) conditions (≈3 × 10 -10 mbar) on clean Si(100) surfaces. For this study, ≈2.0 nm thick Au samples were grown on the substrate surface by molecular beam epitaxy. Thermal annealing was carried out inside the UHV chamber at temperature ≈500 °C and following this, nearly square shaped Au xSi 1-x nano structures of average length ≈48 nm were formed. A ≈2 nm Ge film was further deposited on the above surface while the substrate was kept at a temperature of ≈500 °C. Well ordered Au-Ge nanostructures where Au and Ge residing side by side (lobe-lobe structures) were formed. In our systematic studies, we show that, gold-silicide nanoalloy formation at the substrate (Si) surface is necessary for forming phase separated Au-Ge bilobed nanostructures. These results show that the Au-Ge bonding is unstable in nature. Electron microscopy (TEM, STEM-EDS, SEM) studies were carried out to determine the structure of Au-Ge nano systems. Rutherford backscattering spectrometry measurements show gold inter-diffusion into substrate while it is absent for Ge. © 2012 American Institute of Physics.