Randomized controlled trials (RCTs) are the gold standard method for developing evidence-based medicine in inflammatory bowel disease (IBD). Methodological problems in RCTs in IBD concern different aspects such as the definition of the study population due to the extreme variability of patients with IBD, the indices of disease activity, a clearly defined outcome, the environmental risk factors (i.e smoking behaviour) that may influence the randomization, the heterogeneous placebo rate of remission and the different statistical methods used to analyze the results. It is important that trials are designed efficiently, done well and complement clinical practice with a careful subject selection, standardization of disease activity indices, and precise outcome measurement in order to continue the improvement of the IBD research process.