Abstract Background The EpiCom-study investigates a possible East-West-gradient in Europe in the incidence of IBD and the association with environmental factors. A secured web-based database is used to facilitate and centralize data registration. Aim To construct and validate a web-based inception cohort database available in both English and Russian language. Method The EpiCom database has been constructed in collaboration with all 34 participating centers. The database was translated into Russian using forward translation, patient questionnaires were translated by simplified forward-backward translation. Data insertion implies fulfillment of international diagnostic criteria, disease activity, medical therapy, quality of life, work productivity and activity impairment, outcome of pregnancy, surgery, cancer and death. Data is secured by the WinLog3 System, developed in cooperation with the Danish Data Protection Agency. Validation of the database has been performed in two consecutive rounds, each followed by corrections in accordance with comments. Results The EpiCom database fulfills the requirements of the participating countries’ local data security agencies by being stored at a single location. The database was found overall to be “good” or “very good” by 81% of the participants after the second validation round and the general applicability of the database was evaluated as “good” or “very good” by 77%. In the inclusion period January 1st –December 31st 2010 1336 IBD patients have been included in the database. Conclusion A user-friendly, tailor-made and secure web-based inception cohort database has been successfully constructed, facilitating remote data input. The incidence of IBD in 23 European countries can be found at www.epicom-ecco.eu.