 The present study protocol describes the trial design of a primary care intervention cohort study, which examines whether an extended, multi-professional physical activity referral (PAR) intervention is more effective in enhancing and maintaining self-reported physical activity than physical activity prescription in usual care. The study targets patients with newly diagnosed hypertension and/or type 2 diabetes. Secondary outcomes include: need of pharmacological therapy; blood pressure/plasma glucose; physical fitness and anthropometric variables; mental health; health related quality of life; and cost-effectiveness.