Infrared spectroscopy of saliva is an express and non-invasive method of analysis, applicable for diagnostics of various diseases and for studying metabolic processes and adaptive changes in the body. The goal of this study was to determine possibility of analyzing the products of lipid peroxidation (LPO) by using IR spectroscopy of saliva on the example of oncological diseases. The study involved 203 patients with lung cancer (n = 40), breast cancer (n = 50) and the control group (n = 113). Saliva samples were collected in the morning after overnight fast. The content of LPO products (conjugated dienes, and trienes, Schiff bases, malonic dialdehyde MDA) was determined in all samples and the IR absorption spectra were recorded in the range of 500–4000 cm–1. In the IR spectra, an increase in the intensity of the absorption bands of lipids was observed; it corresponded to an increase in the total lipid content and correlated with the content of MDA, and a decrease in the intensity of vibrations of oxygen-containing groups, which corresponded to a negative correlation with secondary LPO products. Apparently, on the IR spectra, we simultaneously register both primary, intermediate, and final LPO products. Statistically significant regression equations were obtained, allowing to estimate the content of intermediate LPO products - conjugated triene, and Schiff bases. The proposed method allows to monitor LPO processes, as well as to characterize the direction of the equilibrium shift in these processes.