Crohn's disease and Ulcerative Colitis are forms of inflammatory bowel disease (IBD), chronic diseases treated with medical and surgical therapy. Patients with IBD are treated with potent immunomodulatory agents, leading to immunosuppression, and the potential for opportunistic infections. In 2014, the ECCO guidelines were released to guide the prevention, diagnosis and treatment of a variety of these opportunistic infections. Since 2014, there have been a number of new agents released as well as a significant expansion in our knowledge of the safety profile of IBD medications. In this article, we review the literature after 2014 regarding opportunistic infections and updates on safety data. Areas covered: We review updates in immunomodulatory therapies for IBD and opportunistic infections since the 2014 ECCO guidelines were published. Expert commentary: The prevention, diagnosis, and treatment of opportunistic infections continue to evolve, as new drugs are approved, and the use of a combination of biologic agents are considered for therapy in clinical trials. What causes some patients to fail to respond to vaccination, or for others to develop severe infections, remains unclear. Improved risk stratification for opportunistic infections in IBD patients and updated ECCO 2014 guidelines would be of significant benefit.