Quartz from deposits and occurrences in the Karelia-Kola region, such as Kyrjala, Fenkina-Lampi, Melomais, Perchatka and Maiskoye, was taken as an example to study the structural heterogeneity of quartz. The study has shown that it is associated with a multi­stage removal of excessive impurities from quartz. Regions that display the most perfect crystalline structure (crystallites) contain the lowest concentrations of impurities, whereas defective regions (damper zones) feature the highest concentrations. HF-treatment dissolves damper zones, while crystallites, formed at specific stages of natural silica purification, remain intact. Their distribution in the quartz samples analyzed was studied to preliminarily assess the environment in which the minerals had formed. The conclusions drawn are consistent with our knowledge of the geological evolution of the deposits, proving that crystallite distribution in quartz is genetically informative. The study of non-crystalline silica to quartz transition shows that before new crystallites are formed silica passes a special stage characterized by a low fluidity limit.