To prospectively compare the diagnostic performance of low-dose computed tomography coronary angiography (CTCA) and cardiac magnetic resonance imaging (CMR) and combinations thereof for the diagnosis of significant coronary stenoses. Forty-three consecutive patients with known or suspected coronary artery disease underwent catheter coronary angiography (CA), dual-source CTCA with prospective electrocardiography-gating, and cardiac CMR (1.5 Tesla). The following tests were analyzed: (1) low-dose CTCA, (2) adenosine stress-rest perfusion-CMR, (3) late gadolinium enhancement (LGE), (4) perfusion-CMR and LGE, (5) low-dose CTCA combined with perfusion-CMR, (5) low-dose CTCA combined with late gadolinium-enhancement, (6) low-dose CTCA combined with perfusion-CMR and LGE. CA served as the standard of reference. CA revealed >50% diameter stenoses in 68/129 (57.7%) coronary arteries in 29/43 (70%) patients. In the patient-based analysis, sensitivity, specificity, NPV and PPV of low-dose CTCA for the detection of significant stenoses were 100, 92.9, 100 and 96.7%, respectively. For perfusion-CMR and LGE, sensitivity, specificity, NPV, PPV, and accuracy were 89.7, 100, 82.4, and 100%, respectively. In the artery-based analysis, sensitivity and NPV of low-dose CTCA was significantly (P < 0.05) higher than that of perfusion-CMR and LGE. All combinations of low-dose CTCA and perfusion-CMR and/or LGE did not improve the diagnostic performance when compared to low-dose CTCA alone. Taking CA as standard of reference, low-dose CTCA outperforms CMR with regard to sensitivity and NPV, whereas CMR is more specific and has a higher PPV than low-dose CTCA.