Background Fluoroscopically guided cardiac catheterisation is an essential tool for diagnosis and treatment of congenital heart disease. Drawbacks include poor soft tissue visualisation and exposure to radiation. We describe the first 16 cases of a novel method of cardiac catheterisation guided by MRI with radiographic support. Methods In our cardiac catheterisation laboratory, we combine magnetic resonance and radiographic imaging facilities. We used MRI to measure flow and morphology, and real-time MRI sequences to visualise balloon angiographic catheters. 12 patients underwent diagnostic cardiac catheterisation, two had interventional cardiac catheterisations, and for two patients, MRI was used to plan radiofrequency ablation for treatment of tachyarrhythmias. Findings In 14 patients, some or all of the cardiac catheterisation was guided by MRI. In two patients undergoing radiofrequency ablation, catheters were manipulated with use of fluoroscopic guidance and outcome was assessed with MRI. All patients received lower amounts of radiation than controls. There was some discrepancy between pulmonary vascular resistance calculated by flow derived from MRI and the traditional Fick method. We were able to superimpose fluoroscopic images of electrophysiology electrode catheters on the three dimensional MRI of the cardiac anatomy. Interpretation We have shown that cardiac catheterisation guided by MRI is safe and practical in a clinical setting, allows better soft tissue visualisation, provides more pertinent physiological information, and results in lower radiation exposure than do fluoroscopically guided procedures. MRI guidance could become the method of choice for diagnostic cardiac catheterisation in patients with congenital heart disease, and an important tool in interventional cardiac catheterisation and radiofrequency ablation.