The site response at 15 stations in the Adana-Ceyhan region (Southern Turkey) is calculated from the recordings of aftershocks of June 27, 1998 Adana-Ceyhan earthquake (M-S=6.2) by using the Standard Spectral Ratio (SSR) and the Horizontal-to-Vertical Spectral Ratio (HVSR) methods. While the two methods are in good harmony at a few stations in determining the site effects, they show differences on the estimated amplifications or on the site resonance frequencies at most stations. It was not clear which one of the two methods underestimates or overestimates the amplification values. We observe that at some stations, where the local site conditions are rather complex, the vertical component records are strongly influenced from the local soil conditions. Thus, the HVSR method fails at these stations. The SSR method underestimates the amplifications at some stations since the rock site, selected as reference site, has its own site response and/or the path correction we applied, considering the geometrical spreading factor only, is insufficient. At the sites where high intensity values were observed, we found high amplifications. The fundamental soil frequencies characterize the damage properties observed in the Adana-Ceyhan earthquake. The fundamental soil frequency is nearly at 1.1 Hz at the Ceyhan site, where severe damage was observed in the 5-6 story buildings, while the fundamental soil frequency is between 3-6 Hz at the Adana site, where damage was in the low-story buildings. Therefore, in addition to inefficient construction practices, it is clear that the resonance effects have also contributed to the observed damage.