In recognition of the benefits of transparent reporting, many peer-reviewed journals require that their authors be prepared to share their raw, unprocessed data with other scientists and/or state the availability of raw data in published articles. But little information on how data should be prepared for publication - or sharing - has emerged. In clinical research patient privacy and consent for use of personal health information are key considerations, but agreed-upon definitions of what constitutes anonymised patient information do not appear to have been established. We aim to address this issue by providing practical guidance for those involved in the publication process, by proposing a minimum standard for de-identifying datasets for the purposes of publication in a peer-reviewed biomedical journal, or sharing with other researchers. Basic advice on file preparation is provided along with procedural guidance on prospective and retrospective publication of raw data, with an emphasis on randomised controlled trials.