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This article presents the results of intraoperative fluorescent diagnostics via the endoscopic system for assessing the quality of photodynamic therapy (PDT) of head and neck cancer. The diagnosis and PDT procedures were performed on the five patients with malignant neoplasms of the vocal cords, lateral surface of the tongue, and trachea and cancer of the left parotid salivary gland. Molecular form of chlorin E6 (Ce6) was intravenously administered with a 1.0–1.1 mg/kg concentration for PDT. Fluorescent diagnostics (FD) was conducted before PDT and after PDT procedures. Control of PDT efficiency was carried out by evaluating the photobleaching of the drug (photosensitizer). The method of intraoperative fluorescent imaging allows determining the exact location of the tumor and its boundaries. The assessment of photosensitizer photobleaching in real time regime allows making quick decisions during PDT procedure, which helps improving the quality of patients’ treatment. The results showed the convenience of endoscopic fluorescent video system in various nosologies of head and neck cancer. Therefore, this diagnostic approach will improve the effectiveness of cancer treatment.