AIM: To identify and describe micro- and ultrastructural thermally induced changes in Baker’s cyst wall associated with the duration of unidirectional uniform heating at 70°C. MATERIALS AND METHODS: We took one full-thickness fragment from each of the 15 Baker’s cysts excised during the operation and divided each fragment into four parts: one was used as a control sample, and the remaining three fragments were placed with the synovial membrane on a thermostat heated to 70°C, with exposure times of 60, 120, and 180 seconds. We used light-optical and electron microscopes for the histomorphological examination of the samples. RESULTS: Two layers of Baker’s cyst wall were identified: inner (synovial) and outer (fibrous). In samples exposed to heat for 60 seconds, the synovial layer was undamaged. In samples exposed to heat for 120 seconds, thermal damage to the cells of the synovial layer and underlying collagen fibers of the fibrous layer was evident. With a heating duration of up to 180 seconds, histomorphological examination revealed signs of damage reaching the middle of the fibrous layer, and signs of deep disorganization of the collagen fibers of the cyst wall were determined at the electron-microscopic level. DISCUSSION: Using light microscopy of intact sections of the cyst wall, we, like other researchers, identified two layers (synovial and fibrous) of different densities, with blood vessels passing through them. The performed experiment suggests that a clinically significant result using Baker’s cyst thermotherapy is achieved when spreading the zone of irreversible coagulation beyond the middle of the fibrous layer of the cyst wall. This, in turn, guarantees damage to the capillary network that provides trophism and proliferation of synoviocytes. The proposed hypothesis corresponds to the paradigm of similar studies on the coagulation of cysts of other localizations. CONCLUSION: The obtained results of the light-optical and electron-microscopic examination of Baker’s cyst wall fragments indicate direct dependence of the depth of thermal coagulation on the duration of heating.