Methods that utilize highly specific antibodies, anti-idiotypic antibodies, various recombinant molecules with antibody properties and immunocorrection and immunoprophylaxis with the help of vaccines are in demand and are intensely developed in the field of biomedicine. Techniques to generate specific single-domain recombinant antibodies (nanobodies) and their derivatives have raised great expectations in the past years. The review considers the recent literature data on the use of nanobodies in basic research, diagnosis, and design of new immunotherapeutic agents. Special sections focus on the prospects of using nanobodies as targeted molecules of microbiota components, the use of anti-idiotypic nanobodies, and a search for promising targets for early diagnosis based on nanobodies.