While travelling through the subsoil layers, earthquake (EQ) generated bedrock motions get modified significantly due to local soil and should be quantified using ground response analysis. Present study concentrates on equivalent linear method of site response analysis in SHAKE2000 software. It is a frequency based analysis tool having default frequency set to 15Hz. While due consideration is given to amplitude, no to very limited information about the frequency content of the input motion to be considered in ground response analysis is available. In the present work, the effect of the maximum frequency of ground motion in site response analysis using SHAKE2000 is examined. Two sets of analyses are carried out in this work based on 30 globally recorded input motions. In the first analyses, input motion up to 15Hz maximum frequency, which is a default value in SHAKE2000 is considered while second analyses are based on considering each of the 30 input motions up to the Nyquist frequency. Comparing the results from the two sets of analyses highlight that selection of maximum frequency in SHAKE2000 has considerable effect in ground motion amplification at different depths. As a result, even the Peak Ground Acceleration (PGA) which controls the building behavior and damage scenario, is going to change considerably even in case same input motion is used in the analysis.