The uniqueness of Minusinsk basin natural complex is determined by its location between the mountain folds of the Kuznetsk Alatau, the Western and Eastern Sayan. The numerous lakes of the territory, being peculiar indicators of the environment, which formed them, are as a rule drainless, and concentrate salts and sulphuretted hydrogen in bottom sediments and lake water. For a century lake mineral water and bottom sediments (therapeutic muds) of several mineralised water bodies of this region have been used medically (health resorts "Lake Shira", "The Uchum", "The Tagarskoe"). The medical effect peculiar both to therapeutic muds and to their organic components, which provide protective, antibacterial, anti-inflammatory, immune modelling properties, was proved. The relevance of the researches of the organic component of the bottom sediments of Minusinsk basin mineral lakes is imposed by the problem of the development of the region's raw material medical base by introducing new resources for the development of modern medical technologies and for getting various peloid concentrates for sanatorium and non-sanatorium usage. Traditional instructions for therapeutic muds analysis, modified methods of extraction of organic components, their gas chromatographic determination and infrared spectroscopy determination are used in the work. The general feature for the most of the studied bottom sediments of lakes is humate-fulvurite type of humus with variations in depth and mineralization. The total organic carbon content varies within the limits of 3.5-9.4% and is determined by the landscape and morphological peculiarities of the lake, the volume of the organic material imported by the land runoff, and the intensity of inner biological processes. The analysis of the group and fraction composition of the organic substances of the bottom sediments showed the predominance of humins (substances, strongly connected with the mineral part of the sediments) in them. Their quantity in several objects exceeds the sum of dissolvable humic acids (HA) and fulvic acids (FA) of substances. In the group of distinguished HA the predominance of fractions, forming a complex with calcium (HA II) is marked. The average content of HA III for varieties of the bottom sediments under study does not exceed 10.3%. The content of the acid-soluble FA (1a) regularly grows with the increase of the concentration of sulphides and mineralization. The indices of the element composition of high-mineralised and medium-mineralised bottom sediments are close; and this fact points at the resemblance of the conditions, which form them. In the composition of organic matter lipins, glycans, polyphenols with the maximal quantity in the sediments of Lake Shunet and Lake Aevskoe can be distinguished. The infrared spectra of the main functional groups of the lipid fraction of the studied bottom sediments and the data of the antioxidant content were obtained and they as a whole determined its balneal value.