Background: Online information retrieval systems have the potential to improve patient care but there are few comparative studies of the impact of online evidence on clinicians' decision-making behaviour in routine clinical work. Methods/design: A randomized controlled parallel design is employed to assess the effectiveness of an online evidence retrieval system, Quick Clinical (QC) in improving clinical decision-making processes in general practice. Eligible clinicians are randomised either to receive access or not to receive access to QC in their consulting rooms for 12 months. Participants complete pre- and post trial surveys. Two-hundred general practitioners are recruited. Participants must be registered to practice in Australia, have a computer with Internet access in their consulting room and use electronic prescribing. Clinicians planning to retire or move to another practice within 12 months or participating in any other clinical trial involving electronic extraction of prescriptions data are excluded from the study. The primary end-points for the study is clinician acceptance and use of QC and the resulting change in decision-making behaviour. The study will examine prescribing patterns related to frequently prescribed medications where there has been a recent significant shift in recommendations regarding their use based upon new evidence. Secondary outcome measures include self-reported changes in diagnosis, patient education, prescriptions written, investigations and referrals. Discussion: A trial under experimental conditions is an effective way of examining the impact of using QC in routine general practice consultations.