Crohn’s Disease and Ulcerative Colitis are associated to relevant social and individual impact in Spain due to its chronic nature and its high prevalence. Furthermore, not only healthcare costs due to both diseases are considerable, but also the indirect costs of the illnesses. The aim of the study was to estimate the burden of the illnesses in terms of costs from the Spanish Health System perspective according to the clinical practice in Spain in 2013. Secondary objectives included the estimation of the indirect costs (societal perspective) and comorbidities’ costs.