A great variety of biotechnological products are now widely used in different ways in agriculture, medicine, food manufacturing and other areas of our life. Industrialized societies now more than ever depend on the use of genetically engineered products, with many of them synthesized using recombinant strains of microorganisms. There is an opinion that microbial strains used in biotechnology are potentially harmful for human health and the environment. Similar to many other countries, we have enacted environmental legislation in an effort to balance the risks and benefits of using biotechnological strains. Although environmental monitoring rules focus mainly on safety assessments of chemicals, the biosafety assessment of microbial strains used in biotechnology is a very important issue as well. This article summarizes 15 years of research on the biotechnological strains of microbes widely used as producers of various biological substances for industrial purposes, and their environmental and biotechnological applications. In our survey, we tried to evaluate possible adverse effects (general toxicity and damage to the immune system, potential sensitizing effects, and damage to normal microbiota) caused by these microbes. It was shown that microscopical fungi of genera Aspergillus, Penicillium and Candida, and some gram-negative bacteria can affect the immune system and disrupt the normal balance of microbial flora of the intestinal tract in rats. The actinomycetes are less dangerous in that they cause fewer side effects. The investigation data obtained can be used to develop safety and hygienic standards for industrial microbes that will help decrease or minimize the occupational risk of infection or damage to the immune system when working with biotechnological strains of microbes.