Since about 20 % of patients with ulcerative colitis (UC) are children and adolescents there is a need for therapeutic options custom-tailored to the children's needs. E. coli Nissle 1917 (EcN) as an evidence-based probiotic alternative to mesalazine (5-ASA) in adult UC remission maintenance is a promising agent for such a therapy. The present open-labelled pilot study was undertaken to investigate the clinical benefit of EcN for maintenance therapy in young UC patients. 34 patients with UC in remission aged between 11 and 18 years were allocated either to EcN (2 capsules o. d., n = 24) or 5-ASA (median 1.5 g/d, n = 10) and observed over one year. As a result, the relapse rate was 25 % (6 / 24) in the EcN group and 30 % (3 / 10) in the 5-ASA group. Data on the patients' global health and development were favourable and no serious adverse events were reported. In conclusion, maintenance therapy for UC with the probiotic EcN is effective also in young patients.