Inflammatory bowel diseases are chronic diseases of the gastrointestinal system followed by numerous complications and extraintestinal manifestations. The two most important types are Crohn's disease and ulcerative colitis with their numerous phenotypes. They present worldwide with differences in epidemiology and exposure to risk factors. The incidence of inflammatory bowel diseases has grown in the recent decades, and they have become an important public health problem. Since no single diagnostic test for confirming ulcerative colitis nor Crohn's disease has been found to date, the diagnosis of inflammatory bowel disease results from multiple diagnostic methods combined with the clinical presentation. Methods of inflammatory bowel disease treatment have dramatically advanced in the last decade due to better understanding of the immune system of mucous membranes and genetics involved in the inflammatory bowel disease pathogenesis by introducing targeted biological therapy and optimizing the existing forms of treatment. The goal of therapy is to achieve and maintain remission of the disease. Since inflammatory bowel disease in most cases develops early in life, it is often necessary to treat patients over a long period of time and adjust the therapy on several occasions with regard to the relapses of the disease, complications or individual patient needs. Drugs administered to these patients are aminosalicylates, glucocorticoids, immunomodulators, antibiotics and, more recently, biological drugs. The main indications for antibiotics in treatment of patients with inflammatory bowel disease are septic complications, symptoms that can be attributed to excessive bacterial growth or perianal disease, and refractory illnesses that do not respond to medication therapy, and if the surgical form of treatment is contraindicated. Beside with medication therapy, another form of treatment for patients with inflammatory bowel disease is surgery. The data considered in this paper are an overview of relevant scientific publications, expert opinions and current practice guidelines.