Introduction Recent evaluations of IT innovations in primary care have highlighted variations between centres and practices in uptake and use. We evaluated whether structural characteristics of a general practice were associated with variations in use of a web-based clinical information system underpinning a Managed Clinical Network in diabetes, between the years 2001 and 2003. Methods Using a computerised audit trail, we calculated the numbers of web-based operations that occurred in each practice, stratified by staff type and year, and adjusted for the numbers of registered diabetic patients. In regression analyses, we determined whether total use was associated with structural characteristics of the practice (total list size, training status, numbers of GPs (general practitioners), mean age of the GPs, numbers of female GPs, level of deprivation of the population and whether staff had received advanced training in diabetes care). Results Initially there were a few practices which made very frequent use of the information system,