Local site effects have an enormous influence on the character of ground motion and play an important role in seismic damage to human being made structures. Several powerful earthquakes have struck Yogyakarta, Indonesia during recent years, one of the destructive which was an Mw 6.3 event that occurred on May 27th, 2006 and caused more than 5,700 fatalities and over 37,000 injuries. Following this event, the single observations of microtremors were densely performed at 274 sites in Yogyakarta City. To provide a good coverage of the study area, the single microtremor observations are designed with a grid spacing of 500 m to the main path of the north–south and east–west of the research area to known in detail the configuration soft rocks and contact hard rock. The predominant periods due to horizontal vertical ratio (HVSRs) are in the range of 0.15–4.00 s. The amplification factor (Ag) and the soil natural frequency (Fg) are generally ranging between 0.70–5.56 and 0.4–3.3 Hz according to results derived from HVSR analysis. It is obviously observed that the thickness of local sediments has great influence on amplification characteristics. In general, the local geology effect is more dominant than the topography effect. The level of soil damage due to the local site effects at the ground deformation location was indicated by the vulnerability index (Kg) and the effective shear strain (γ). Actually, vulnerability index (Kg) varied from 0.6 to 51.3 and the effective shear strain (γ) had values ranging from 300 _ 10_6 to 25,000 _ 10_6 which for γ > 10,000 _ 10_6 catastrophic landslide or very large deformation will be occurred. This study illustrates how the vulnerability index and the effective shear strain could be used to make preliminary assessment of the research area deformed during the earthquake. © Springer International Publishing Switzerland 2014. Show More