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Coronary artery disease (CAD) represents a widespread burden to both individual and public health, steadily rising across the globe. The current guidelines recommend non-invasive anatomical or functional testing prior to invasive procedures. Both coronary computed tomography angiography (cCTA) and stress cardiac magnetic resonance imaging (CMR) are appropriate imaging modalities, which are increasingly used in these patients. Both exhibit excellent safety profiles and high diagnostic accuracy. In the last decade, cCTA image quality has improved, radiation exposure has decreased and functional information such as CT-derived fractional flow reserve or perfusion can complement anatomic evaluation. CMR has become more robust and faster, and advances have been made in functional assessment and tissue characterization allowing for earlier and better risk stratification. This review compares both imaging modalities regarding their strengths and weaknesses in the assessment of CAD and aims to give physicians rationales to select the most appropriate modality for individual patients.