Background The present study protocol describes the trial design of a clinician training intervention to improve physical activity counseling in underserved primary care settings using the 5As. The 5As (Ask, Advise, Agree, Assist, Arrange) are a clinical tool recommended for health behavior counseling in primary care. Methods/Design The study is a two-arm randomized pilot pragmatic trial to examine a primary care clinician communication intervention on use of the 5As in discussion of physical activity in audio-recorded office visits in an ethnically diverse, low-income patient population. The study setting consists of two federally qualified community health centers in Rochester, NY. Eligible clinicians (n=15) are recruited and randomized into two groups. Group 1 clinicians participate in the training intervention first; Group 2 clinicians receive the intervention six months later. The intervention and its outcomes are informed by self-determination theory and principles of patient-centered communication. Assessment of outcomes is blinded. The primary outcome will be the frequency and quality of 5As discussions as judged by evaluating 375 audio-recorded patient visits distributed over baseline and in the post-intervention period (immediately post and at six months). Secondary outcomes will be changes in patients’ perceived competence to increase physical activity (Aim 2) and patients and clinicians beliefs regarding whether pertinent barriers to promoting exercise have been reduced. (Aim 3). Exploratory outcomes (Aim 4) are potential mediators of the intervention’s effect and whether the intervention affects actual enrollment in the community program recommended for exercise. The analysis will use repeated measures (in the form of recorded office visits) from each clinician at each time point and aggregate measures of Groups 1 and 2 over time. Discussion Results will help elucidate the role of 5As communication training for clinicians on counseling for physical activity counseling in primary care. Results will explore the effectiveness of the 5As model linked to community resources for physical activity promotion for underserved groups.