This paper presents an investigation of the impact of a Highly Doped Drain (HDD) implantation after epitaxial deposition on Si1-xGex S/D junction characteristics. While the no HDD diodes exhibit the usual scaling of the leakage current density with Perimeter to Area (P/A) ratio, this is not the case for the HDD diodes, showing a smaller perimeter current density JP for smaller window size structures, corresponding with larger P/A. This points to a lower density of surface states at the Shallow Trench Isolation (STI)/silicon interface, which could result from a lower compressive stress. In order to examine the role of the HDD implantation damage, Transmission Electron Microscopy (TEM) inspections have been undertaken, which demonstrate the presence of stacking faults in small active SiGe regions. These defects give rise to local strain relaxation and, therefore, could be at the origin of the lower STI/Si interface state density. The window size effect then comes from the active area dependence of the implantation defect formation.