For the first time, the chronic inhalation effect of aliphatic hydrocarbons (HC) in low concentrations on metabolic profiles of low molecular weight organic compounds including free (FFA) and esterified (EFA) fatty acids in rats brain and liver was studied. Gas and liquid chromatography-mass spectrometry was used as analytical methods. The list of hydrocarbons includes hexane, heptane, octane, nonane and decane in various ratios. Changes in profiles of low-molecular compounds in the brain were detected under the action of a mixture of HCs in a concentration of 160 ± 20.5 mg/m3 for 90 days, while the action of the HCs mixture at lower concentrations of 31.4 ± 5.6 mg/m3 and 5.2 ± 1.08 mg/m3 only leads to minor changes in profiles. A significant increase in lysophospholipids concentrations, mainly of lysophosphatidylcholine, in the extract from the brain and blood plasma was revealed. The increase in the content of lysophospholipids in brain tissues can be considered as a consequence of the destruction of cell membranes, specific to neurodegenerative processes. At the same time, an increase in the lysophosphatidylcholine concentration in the brain is accompanied by a statistically significant decrease in the concentration of glycerol-3-phosphate and is not followed by changes in the concentrations of glycerophosphocholine, glycerophosphoethanolamine, choline, acetylcholine, FFA, or lysophosphatidic acid. It was shown that concentrations of lysophosphatidylcholine and lysophosphatidylethanamine, referred to the concentrations of glycerophosphocholine and glycerophosphoethanolamine in blood plasma, may serve as potential markers of the effect of HC on the brain.