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Background: High amounts of coronary artery calcium (CAC) pose challenges in interpretation of coronary CT angiography (CCTA). The accuracy of stenosis assessment by CCTA in patients with very extensive CAC is uncertain. Methods: Retrospective study was performed including patients who underwent clinically directed CCTA with CAC score >1000 and invasive coronary angiography within 90 days. Segmental stenosis on CCTA was graded by visual inspection with two-observer consensus using categories of 0%, 1–24%, 25–49%, 50–69%, 70–99%, 100% stenosis, or uninterpretable. Blinded quantitative coronary angiography (QCA) was performed on all segments with stenosis ≥25% by CCTA. The primary outcome was vessel-based agreement between CCTA and QCA, using significant stenosis defined by diameter stenosis ≥70%. Secondary analyses on a per-patient basis and inclusive of uninterpretable segments were performed. Results: 726 segments with stenosis ≥25% in 346 vessels within 119 patients were analyzed. Median coronary calcium score was 1616 (1221–2118). CCTA identification of QCA-based stenosis resulted in a per-vessel sensitivity of 79%, specificity of 75%, positive predictive value (PPV) of 45%, negative predictive value (NPV) of 93%, and accuracy 76% (68 false positive and 15 false negative). Per-patient analysis had sensitivity 94%, specificity 55%, PPV 63%, NPV 92%, and accuracy 72% (30 false-positive and 3 false-negative). Inclusion of uninterpretable segments had variable effect on sensitivity and specificity, depending on whether they are considered as significant or non-significant stenosis. Conclusions: In patients with very extensive CAC (>1000 Agatston units), CCTA retained a negative predictive value ​> ​90% to identify lack of significant stenosis on a per-vessel and per-patient level, but frequently overestimated stenosis.