Low efficiency of the standard THz-TDS method for the detection and identification of substances is demonstrated. For this purpose, we use a few examples. In the first example, we model the noisy THz signals transmitted through the amphetamine-type stimulant in real conditions. Namely, with a temperature 18° C, the relative humidity of about 50 % and the distance between the parabolic mirror and the object about of 3.5 meters. We show that the standard THz-TDS method reveals the spectral features of many neutral substances and explosives in the noisy THz signals from the illicit stimulant MA, at the same time this method is not able to detect the presence of this stimulant in the noisy signals. The second example is the detection and identification of plastids with inhomogeneous surface in reflection mode. We show that inhomogeneous surface distorts spectral characteristics of the reflected THz signal main pulse, which cannot be used for the detection and identification of the plastids by means of the THz TDS method. In the last example we show that even under laboratory conditions (at short distance from the receiver), THz TDS detects in the semiconductors the absorption frequencies, which belong to both hazardous and neutral substances. To overcome this disadvantage, we propose to use the time-dependent spectrum of the THz pulse, transmitted through or reflected from a substance. For quality assessment of the presence of the standard substance absorption frequency in the signal under analysis, we use time-dependent integral correlation criteria. The influence of aperture placed in front of the sample on spectral properties of silicon wafers with different resistivity is demonstrated as well.Keywords: reflected and transmitted THz pulse, noisy THz pulse, method of spectral dynamics analysis, integral correlation criteria, identification of explosives and drugs. *vatro@cs.msu.ru; phone 7 495 939-5255; fax 7 495 939-2597