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Medical waste is a special kind of hazardous materials, which disposal leads to considerable pollution of the environment. The widespread method of medical waste disposal is thermal treatment (pyrolysis or incineration), which gives appropriate transformation of waste into a safe form (ash) and energy. On the other hand, the thermal treatment of medical waste that contain chlorine leads to the formation of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), most toxic representatives of organic pollutants. This paper analyses various mechanisms of the PCDD/Fs formation during thermal treatment of chlorine-containing medical waste. The features of these mechanisms are considered. It is shown that in pyrolytic conditions the PCDD/Fs yield is much lower than under direct incineration. Optimal temperature conditions are determined, under which the formation of these compounds is minimal.