Since Janus kinases mediate the effects of numerous inflammatory cytokines, various side effects are observed during treatment with JAK inhibitors that inhibit these kinases. Infections are the most common side effects. The development of malignancy, venous thromboembolism, major cardiovascular adverse events, nausea, acne, and various laboratory abnormalities has also been observed with the use of JAK inhibitors. With the long-term use of JAK inhibitors, their safety, toxicity and side effect profiles are better understood.