All chemical compounds may undergo a variety of processes resulting from chemical, biological or photochemical reactions. Depending on the environmental compartment in which organic compounds are present (e.g. soil, benthic sediments, surface and ground waters), they can undergo slow changes resulting from different chemical, physical, biological or photochemical processes. The problem of intermediate products that form during the degradation of substances, the toxicity of substances that are the products of organic compounds degradation, and the ways to identify such substances are discussed.