Background. In many countries exercise prescriptions are used in an attempt to initiate a physically active lifestyle in sedentary populations. Previous studies have primarily evaluated low intensive exercise prescription interventions and found moderately positive effects on physical activity and aerobic fitness. In a highly intensive Danish exercise prescription scheme called 'Exercise on Prescription' (EoP) the general practitioners can prescribe EoP to sedentary patients with lifestyle diseases. The aim of this randomized trial is to assess the short- and long-term effects of the EoP scheme. Thus, the aim of this paper is to describe the randomized controlled trial designed for evaluating effectiveness of EoP, and to present results from validations of outcome measures. Methods/Design. EoP involves a 16-week supervised training intervention and five counselling sessions (health profiles). All patients referred to EoP were eligible for the trial and were offered participation during the baseline health profile. Comparisons between the EoP group and the control group were made at baseline, and after four and ten months. Physiological measures used were maximal oxygen uptake (VO2max), glycosylated haemoglobin (HbA1c), bodyweight, and BMI. Patient-reported measures used were physical activity, health-related quality of life, amount and intensity of exercise, compliance with national guidelines for physical activity, and physical fitness. The validation of the cycle ergometer test found a strong correlation between maximal work capacity and VO2max, and acceptable test-retest reliability at group level. Calibration of the HbA1c apparatus was stable over ten weeks with minimal use, and test-retest reliability was good. High agreement percents were found for test-retest reliability for the self-administered questionnaire. Discussion. The trial is designed to provide information about the effectiveness of the EoP scheme. The trial is part of a health technology assessment of EoP, which besides the effectiveness covers the patient perspective, the organization, and the health economy. All three methods validated were found useful for the EoP trial.