Myocardial perfusion imaging (MPI) has been a valuable diagnostic and prognosticating tool for decades, but recently it has been challenged by the growing evidence about either comparable or superior diagnostic and prognostic value of computed tomography (CT)-based anatomical imaging modalities. Although there are some studies suggesting synergy and potential for combined use of these modalities to better diagnose coronary artery disease (CAD), it is important to evaluate these approaches separately, given cost and other restraints. This review compares the noninvasive anatomical imaging modalities of coronary artery calcium scoring and coronary CT angiography to the functional assessment modality of MPI in the diagnosis and prognostication of significant CAD in symptomatic patients. A large number of studies investigating this subject are analyzed with a critical look on the evidence, underlying the strengths and limitations. Although the overall findings of the presented studies are favoring the use of CT-based anatomical imaging modalities over MPI in the diagnosis and prognosticating of CAD, the lack of a high number of large- scale, multicenter randomized controlled studies limits the generalizability of this early evidence. Further studies comparing the short- and long-term clinical outcomes and cost-effectiveness of these tests are required to determine their optimal role in the management of symptomatic patients with suspected CAD.