In this paper, efficiency of alternative geophysical techniques for site response is evaluated in two sedimentary basins on the North Anatolian Fault Zone. For this purpose, fundamental frequencies of soils and corresponding amplitudes obtained from empirical horizontal-to-vertical spectral ratio curves from microtremors, weak motions and strong motions are compared with results from one-dimensional theoretical transfer functions. Theoretical transfer functions are computed using S-wave velocity profiles derived from array observations of the microtremor wavefield. Our results are consistent with studies from other regions in that the fundamental frequencies from microtremors, weak motions and theoretical transfer functions are mostly in agreement with each other although some discrepancies are observed. Even though important information about fundamental resonance frequency can be derived from horizontal-to-vertical spectral ratios, observed amplitudes do not yield consistent results with the theoretical amplification factors. Thus, the use of horizontal-to-vertical spectral ratio amplitudes is not recommended for estimation of amplification factors. Based on our observations, complementary use of alternative methods for site response is recommended.