In the present paper we consider the problem of innovative treatment of systemic autoiminune diseases for example, rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). The use of biological therapy is suitable for severe rheumatoid arthritis and promotes remission in 25-30% of cases. Application biological therapy (as anti-B cell therapy) in cases of systemic lupus erythematosus severe forms can reduce the immuno activity level, and also leads to the regression of secondary vasculitis in lung tissue and renal parenchyma. The analysis of drugs and principles of treatment of rheumatoid arthritis and systemic lupus erythematosus was done. Particular attention is paid to the safety and efficacy of biological agents and synthetic base anti-inflammatory drugs.