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Objectives The aim of this study was to investigate the individual and combined accuracy of dynamic computed tomography (CT) myocardial perfusion imaging (MPI) and computed tomography angiography (CTA) fractional flow reserve (FFR) for the identification of functionally relevant coronary artery disease (CAD). Background Coronary CTA has become an established diagnostic test for ruling out CAD, but it does not allow interpretation of the hemodynamic severity of stenotic lesions. Two recently introduced functional CT techniques are dynamic MPI and CTA FFR using computational fluid dynamics. Methods From 2 institutions, 74 patients (n = 62 men, mean age 61 years) planned for invasive angiography with invasive FFR measurement in 142 vessels underwent CTA imaging and dynamic CT MPI during adenosine vasodilation. A patient-specific myocardial blood flow index was calculated, normalized to remote myocardial global left ventricular blood flow. CTA FFR was computed using an on-site, clinician-operated application. Using binary regression, a single functional CT variable was created combining both CT MPI and CTA FFR. Finally, stepwise diagnostic work-up of CTA FFR with selective use of CT MPI was simulated. The diagnostic performance of CT MPI, CTA FFR, and CT MPI integrated with CTA FFR was evaluated using C statistics with invasive FFR, with a threshold of 0.80 as a reference. Results Sensitivity, specificity, and accuracy were 73% (95% confidence interval [CI]: 61% to 86%), 68% (95% CI: 56% to 80%), and 70% (95% CI: 62% to 79%) for CT MPI and 82% (95% CI: 72% to 92%), 60% (95% CI: 48% to 72%), and 70% (63% to 80%) for CTA FFR. For CT MPI integrated with CTA FFR, diagnostic accuracy was 79% (95% CI: 71% to 87%), with improvement of the area under the curve from 0.78 to 0.85 (p Conclusions CT MPI and CTA FFR both identify functionally significant CAD, with comparable accuracy. Diagnostic performance can be improved by combining the techniques. A stepwise approach, reserving CT MPI for intermediate CTA FFR results, also improves diagnostic performance while omitting nearly one-half of the population from CT MPI examinations.