The estimation of the impulse response of a transfer system by the cross-spectral technique is very popular and most FFT analyzers are equipped with that function. However, the deformation of the impulse response in the process of estimation is not yet known. The deformation of the impulse response is caused by the use of the time window in the FFT as the DFT of a windowed waveform is the convolution of the spectrum of the waveform and the spectrum of the time window. This paper first describes the theoretical analysis on the deformation. Next, the result is verified by the computer simulation. The estimation errors are also investigated for various types of time windows. According to the investigation, the deformation is significant if the duration of the impulse response (the reverberation time) is longer than 1/4 of the window length. Finally, the use of the rectangular window in order to not deform the impulse response by shortening the length of window for the source signal is described.