Comparative studies of different microbial strains used in biotechnology as potentially hazardous for human health agents demonstrated their ability to cause adverse effects such as toxicity, immunotropic action, sensitization, and alteration of normal intestinal microflora in rats. It was shown that certain microscopic fungi of genera Aspergillus, Penicillum, and Candida as well as some gram-negative bacteria can affect the immune system and disturb the balance of microflora in rat intestines. Actinomycetes were found to produce minimal adverse effects. These observations can be used to elaborate hygienic safety standards for the work with industrial microorganisms and thereby reduce or minimize the risk of occupational infection and immune disorders.