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A process is disclosed for treating biologically contaminated substrates and for cleaning and decontaminating containers and equipment soiled with said substrate within a closed installation in which both substrates and containers and equipment are treated in such a way that biologically active cellular substances cannot reach the waste water system nor the atmosphere together with the substrate itself nor with the rinsing water used to clean the containers and equipment. After being emptied, the containers and equipment are cleaned in several steps (2, 4, 6, 8) with rinsing water (3, 5, 7, 23) and cleaning additives in a collecting tank (20), then are dry-heated (9) up to temperatures above 200 DEG C, inactivating any biologically active cellular substances that may still adhere to the containers and equipment. The liquid and solid phases of the substrate are separated in the collecting tank and in the cleaning liquids, and the dry substrate or a strongly concentrated substrate are disposed of by being subsequently incinerated in a combustion chamber (32). The "thin phase" (22) formed by the effluents of the substrate concentration process (21) and by overflow water from the rinsing water tanks (3, 5, 7) is purified by appropriate processes until it may be reused as rinsing water, whereas the partial volume of "thin phase" (22) that may not be used as rinsing water is completely purified by an appropriate process from all biologically active cellular substances, so that after a final check for residual impurities (26) it may be discharged without danger into waste water or reused with a new batch of substrate (11). Air or steam-air mixtures that leave the treatment chambers and rinsing water tanks are subsequently decontaminated by a thermal process.