The characteristics of the strong ground motion accelerograms from the 1.999 Kocaeli earthquake are investigated in detail in this study. The emphasis is on the comparison of the response spectra for the fault normal (FN) and fault parallel (FP) components of the ground motions. The results show that the near-fault records with directivity effects characterize themselves with increased base shear demands rather than increased displacement demands for both the FN and FP components and a narrower velocity sensitive region for the FN component. This study also shows that the effectiveness of base isolation may vary from site to site and for a given site, from component to component. The site effects in the Marmara region during the 1999 Kocaeli earthquake are examined. Site amplifications are predicted by the classical spectral ratio (CSR) and the receiver function (R-F) methods. The CSR method gives higher estimates for the site amplifications compared to the RF method and is in better conformity with the observed damage during the Kocaeli earthquake. The districts of Istanbul that are especially susceptible to site amplification hazard are determined. It is apparent from the results that the site amplification hazard risk is the highest for Avcilar and Bakirkoy districts. This study also shows that for sites which have the risk of soil amplification for long-period structures, liquefaction may not be beneficial as a natural base isolator, and may result in shifting the eigenperiod of the low- and mid-rise structures to the critical periods with high site amplifications. This may be especially the case for Avcilar and Bakirkoy districts. In Fatih, Bakirkoy, and Cekmece districts, the predominant period of the ground motion is calculated to be very close to the eigenperiods of the typical residential buildings. Therefore, these three districts are expected to experience heavier damages in future earthquakes due to resonance effects.