Background Magnetic Resonance Imaging (MRI) of patients with implanted cardiac devices is currently considered hazardous due to potential for electromagnetic interference to the patient and pacemaker system. With approximately 60 million MRI scans performed worldwide per year, an estimated majority of pacemaker patients may develop an indication for an MRI during the lifetime of their pacemakers, suggesting that safe use of pacemakers in the MRI environment would be clinically valuable. A new pacing system (Medtronic EnRhythm MRI™ SureScan™ and CapSureFix MRI™ leads) has been designed and pre-clinically tested for safe use in the MRI environment. The EnRhythm MRI study is designed to confirm the safety and efficacy of this new pacing system. Methods The EnRhythm MRI study is a prospective, randomized controlled, unblinded clinical trial to confirm the safety and efficacy of MRI at 1.5 Tesla in patients implanted with a specifically designed pacemaker and lead system. The patients have standard indications for dual chamber pacemaker implantation. Successfully implanted patients are randomized in a 2:1 ratio to undergo MRI (MRI group) or to have no MRI scan (control group) at 9–12 weeks after pacemaker system implantation. Magnetic resonance (MR) scanning includes 14 head and lumbar scan sequences representing clinically relevant scans while maximizing the gradient slew rate up to 200 T/m/s, and/or the transmitted radiofrequency (RF) power up to SAR (specific absorption rate) levels of 2 W/kg body weight (upper limit of normal operating mode). Full interrogation of all device information and sensing and capture function are measured at device implantation, every follow-up and before and immediately after MRI in the MRI group and at the same time points in the control group. Complete pacemaker and lead evaluations are also done at one week and one month after the scan for the MRI and control group patients. The primary endpoint is safe and successful completion of the MRI scan as measured by freedom from both MRI-procedure related complications and clinically significant changes in the sensing and capture function of the leads. Results Results will be communicated after approximately 156 and 470 patients have completed 4 months of follow-up. Trial Registration ClinicalTrials.gov identifier: NCT00433654.