Background: Access to high quality evidence is mandatory in high quality university medicine. The Frankfurt University hospital granted the implementation of an online course teaching the five steps of evidence-based medicine (EBM) using systematic reviews beginning in 2009. A randomized controlled trial was conducted to investigate the effects of this online course on critical appraisal skills, basic scientific knowledge and attitude towards EBM. Methods: All junior house officers (JHOs) who began their employment since January 2008 are being contacted to join the EBM Unity course. All participants are being randomized to either the intervention group (starting the course immediately after signing up) or to the control group (delaying the start for three months). Each group is receiving pre-and post-course questionnaires, structured assignments after each module and subjective evaluation forms before and after the course and after each module. Non-responders are also being investigated. Results: Thirty-seven (14 F, 23 M) out of 88 eligible JHOs are participating in the EBM Unity course at present. There are 18 JHOs randomized into the intervention group currently proceeding with the course. Thirty participants (81%) are presently going through their first year of further training in their clinical field. Conclusions: Up to now the implementation of an online course in evidence-based medicine can be considered successful. Preliminary analyses of some pretest questionnaires show concordantly the lack of knowledge of evidence-based medicine, critical appraisal of systematic reviews and basic scientific knowledge. The effects of the EBM Unity course (pre-versus post-course) will be available and presented in October 2009 along with the analysis of the subjective pre-and post-course evaluation.