Cardiac magnetic resonance (MR) imaging of mice is a valuable tool for the precise in vivo diagnosis and prognosis of heart defects. This detailed protocol describes the method of cardiac MR imaging in mice step by step. A series of MR images captures the contractile function of the mouse heart and post-processing of the image data yields morphometric parameters (myocardial mass, myocardial wall thickness, ventricular end-systolic and end-diastolic volume) as well as functional parameters (stroke volume and ejection fraction). This protocol may also serve as a starting point for MR imaging of rats, by using larger image dimensions (field-of-view) and MR hardware suitable for larger animals.