AIMS: To describe and evaluate the use of an Internet-based study protocol in a multicentre study of genetic risk factors in anticoagulant treatment. METHODS: A web-based study protocol, similar to existing anticoagulation medical record systems, was developed for entry of clinical data. It was also supplied with a separate interface for study monitoring. Measures were taken to assure the confidentiality of transferred data. In addition, software modifications were made to enable automated transfer of clinical data from an existing medical record system to the study database. RESULTS: The system has been in use since March 2002, and at present 39 centres have included 909 patients with a dropout rate of 2.8%. The need for education of participating clinicians has been satisfactorily provided for by means of written instructions and telephone support. CONCLUSIONS: Our study demonstrates the usability of Internet-based data acquisition techniques in a full-scale multicentre clinical trial. The main advantages of such a protocol are automated data validation and standardization, fast data transfer independent of geographical distance, user feedback, synchronization of protocol updates and automatic data formatting facilitating statistical analyses. Safety and accessibility are possibly cumbersome areas and should be addressed duly.