BACKGROUND: Brief motivational interventions that have been provided in addition to routine primary care have changed adolescent health behaviors. Whether health screening and motivational-interviewing-based counseling provided by clinicians during routine care can change behaviors is unknown. METHODS: Healthy Teens was a primary care, office-system intervention to support efficient, patient-centered counseling at well visits. Healthy Teens utilized a personal digital assistant (PDA)-based screener that provided the clinician with information about a teen's health risks and motivation to change. Changes in adolescent self-report of diet and activity health behaviors 6 months later were assessed in two cross-sectional samples of teens from five rural practices in 2005 and 2006. Usual-care subjects (N=148) were recruited at well visits prior to the intervention, and the Healthy Teens subjects (N=136) were recruited at well visits after the Healthy Teens system was well established. RESULTS: At 6-month follow-up, the Healthy Teens group had significantly increased self-reported exercise levels and milk-product intake. In the models exploring covariates, the only significant predictors for improvement in exercise levels were intervention-group status (p=0.009) and post-visit interest in making a change (p=0.015). Interest in changing predicted increased milk intake (p=0.028) in both groups. When teens planned an action related to nutrition, physical activity, or both after a well visit, Healthy Teens participants were more likely to report multiple planned actions (68% Healthy Teens vs 32% usual care, p<0.05). CONCLUSIONS: Changes in office systems using low-cost technology to screen adolescents and promote patient-centered counseling appear to influence teens to increase exercise and milk intake.