Background: Although the costs of treating inflammatory bowel disease (IBD) in developed countries are well established, they remain largely unknown in countries with recent histories of socio-economic transition including Serbia. Objective: To estimate the costs of treatment including the resources used by patients with IBD in Serbia from a societal perspective. This includes both Crohn’s disease and ulcerative colitis. Methods: This cost-of-illness study was conducted to identify direct, indirect and out-of-pocket costs of treating patients with IBD in Serbia. Patients with IBD (n = 112) completed a semi-structured questionnaire with data concerning their utilisation of heath-care resources and illness-related expenditures. All costs were calculated in Republic of Serbia dinars (RSD) at a 1-year level (2014) and subsequently converted to Euros. Median values and ranges were reported to avoid potential distortions associated with mean costs. Results: Median total direct costs and total indirect costs per patient per year in patients with Crohn’s disease were 192,614.32RSD (€1602.97) and 28,014.00RSD (€233.13) and 142,267.15RSD (€1183.97) and 21,436.00RSD (€178.39), respectively, in patients with ulcerative colitis. In both groups, the greatest component of direct costs was hospitalisation. Conclusions: Costs of IBD in Serbia are lower than in more developed countries for two reasons. These include the fact that expensive biological therapy is currently under-utilised in Serbia and prices of health services are largely controlled by the State at a low level. The under-utilisation of biologicals may change with the advent of biosimilars at increasingly lower prices.