This study presents the findings of the structural health monitoring and the real time system identification of one of the first large scale building instrumentations in Turkey for earthquake safety. Within this context, a thorough review of steps in the instrumentation, monitoring is presented and seismic performance evaluation of structures using both nonlinear pushover and nonlinear dynamic time history analysis is carried out. The sensor locations are determined using the optimal sensor placement techniques used in NASA for on orbit modal identification of large space structures. System identification is carried out via the stochastic subspace technique. The results of the study show that under ambient vibrations, stocky buildings can be substantially stiffer than what is predicted by the finite element models due to the presence of a large number of partitioning walls. However, in a severe earthquake, it will not be safe to rely on this resistance due to the fact that once the partitioning walls crack, the bare frame contributes to the lateral stiffness of the building alone. Consequently, the periods obtained from system identification will be closer to those obtained from the FE analysis. A technique to control the validity of the proportional damping assumption is employed that checks the presence of phase difference in displacements of different stories obtained from band pass filtered records and it is confirmed that the "proportional damping assumption" is valid for this structure. Two different techniques are implemented for identifying the influence of the soil structure interaction. The first technique uses the transfer function between the roof and the basement in both directions. The second technique uses a pre-whitening filter on the data obtained from both the basement and the roof. Subsequently the impulse response function is computed from the scaled cross correlation between the input and the output. The overall results showed that the structure will satisfy the life safety performance level in a future earthquake but some soil structure interaction effects should be expected in the North South direction.