The article reports the results of a study of quartz in shungite rocks of the Shunga, Zazhogino and Maksovo deposits in the Onega Paleoproterozoic Basin located in the Karelian Craton in the southeastern part of the Baltic Shield. Silica is one of the main components of shungite rocks (C_org 35–80 %) and lydites (C_org up to 5 %), in which it forms two morphological types: epigenetic vein quartz and authigenic quartz. The rocks retain signs of delayed diagenesis of organic and siliceous matter: high dispersion of mineral segregations, dyscrystalline mineral matter, globular and other metacolloidal forms of segregations, which indicates the colloidal origin of authigenic quartz. The values of the (O/Si)_at ratio were determined for morphologically different segregations of quartz in shungite rocks. The results of the study suggest that the structural features of authigenic quartz arose during the early stages of lithogenesis in the context of active interaction with organic matter. Most likely, the organic matter partially or fully retained its bondage to the siliceous matter of shungite rocks in the process of catagenetic transformations.