We present the novel results of studying tissue metabolites of the ear-nose-throat organs (pathological and relatively healthy mucosal tissues) during heating and thermal exposure using gas spectrometers of the terahertz (THz) frequency range based on non-stationary effects. Tissue metabolites of the ear-nose-throat organs obtained during surgery according to strict medical indications have been studied for the first time in the world. All the tissues used in the samples were histological verified for confirming the morphological diagnosis. For obtaining a unified picture, chemical compounds appearing during thermal decomposition of pathological and relatively healthy tissues were identified using the spectroscopic approach, with mandatory histological verification of the samples. The obtained results demonstrate that a powerful research tool has been proposed for evaluation of metabolites in otorhinolaryngology with detection of diseases markers.