Recently, physical and physicochemical methods of analysis, such as gas chromatography, mass spectrometry, IR and THz spectroscopy, are increasingly used in medical diagnostics. With their help, it is possible to identify substances, the so-called metabolites, characteristic of a particular disease. Compiling a metabolic profile will speed up and facilitate the process of diagnosing a disease, assess the stage and etiology, and predict therapy. It is relevant to study the state of the ear-nose-throat (ENT) organs, as one of the main ways of penetration into the human body of infections, viruses, etc. But in the literature and the database of human metabolomes, there are no data on metabolites in diseases of the ENT organs. The work is devoted to analyzing the metabolites composition of the ENT organs tissues by high-resolution THz spectroscopy and the comparison of the metabolite’s composition, which are formed during thermal decomposition of a relatively healthy mucosa, a sphenoid sinus polyp and a cyst of the maxillary sinus. The studies were carried out using high-resolution THz spectrometers developed by the authors, operating in the range of 118-178 GHz. Substances were identified using electronic databases. A qualitative analysis of the chemical composition of the thermal decomposition products and a comparison of the obtained spectra of substances and the number of absorption lines of samples to evaluate the metabolites were performed. Analysis of the results showed that all samples contained substances such as alcihols, nitriles, sulfur compounds. However, in the spectrum of a relatively healthy mucosa, the number of absorption lines of these substances is much less than in the spectra of a polyp and a cyst, which indicates their lower concentration. In addition, absorption lines appear in the spectra of the polyp and cyst, corresponding to substances such as ketones, nitriles, aldehydes, acids, at that their concentrations differ significantly. Thus, the potential possibility of using high-resolution THz spectroscopy for the analysis of the composition of metabolites of ENT tissues has been shown.