OBJECTIVES: This study sought to compare the diagnostic performance of a multidetector computed tomography (MDCT) integrated protocol (IP) including coronary angiography (CTA) and stress-rest perfusion (CTP) with cardiac magnetic resonance myocardial perfusion imaging (CMR-Perf) for detection of functionally significant coronary artery disease (CAD). BACKGROUND: MDCT stress-rest perfusion methods were recently described as adjunctive tools to improve CTA accuracy for detection of functionally significant CAD. However, only a few studies compared these MDCT-IP with other clinically validated perfusion techniques like CMR-Perf. Furthermore, CTP has never been validated against the invasive reference standard, fractional flow reserve (FFR), in patients with suspected CAD. METHODS: 101 symptomatic patients with suspected CAD (62 ± 8.0 years, 67% males) and intermediate/high pre-test probability underwent MDCT, CMR and invasive coronary angiography. Functionally significant CAD was defined by the presence of occlusive/subocclusive stenoses or FFR measurements ≤0.80 in vessels >2mm. RESULTS: On a patient-based model, the MDCT-IP had a sensitivity, specificity, positive and negative predictive values of 89%, 83%, 80% and 90%, respectively (global accuracy 85%). These results were closely related with those achieved by CMR-Perf: 89%, 88%, 85% and 91%, respectively (global accuracy 88%). When comparing test accuracies using noninferiority analysis, differences greater than 11% in favour of CMR-Perf can be confidently excluded. CONCLUSIONS: MDCT protocols integrating CTA and stress-rest perfusion detect functionally significant CAD with similar accuracy as CMR-Perf. Both approaches yield a very good accuracy. Integration of CTP and CTA improves MDCT performance for the detection of relevant CAD in intermediate to high pre-test probability populations.