This paper investigates the effectiveness of widely used identification methods to identify the response of seismically isolated structures supported on bearings with bilinear behavior. The paper shows that while both time domain and frequency domain methods predict with high accuracy the modal characteristics of structures isolated by linear isolation system, their performance degrades appreciably when the isolation system exhibits bilinear behavior even when its strength assumes moderate values (say 5% of the weight). The paper also shows that the natural period of isolated structure that results from bilinear isolation systems can be satisfactorily predicted with wavelet analysis.