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Abstract To evaluate mosaic perfusion patterns and vascular lesions in patients with chronic thromboembolic pulmonary hypertension (CTEPH) using C-Arm computed tomography (CACT) compared to computed tomography pulmonary angiography (CTPA). We included 41 patients (18 female; mean age 59.9 ± 18.3 years) with confirmed CTEPH who underwent CACT and CTPA within 21 days (average 5.3 ± 5.2). Two readers (R1; R2) independently evaluated datasets from both imaging techniques for mosaic perfusion patterns and presence of CTEPH-typical vascular lesions. The number of pulmonary arterial segments with typical findings was evaluated and the percentage of affected segments was calculated and categorized: < 25%; 25–49%; 50–75%; < 75% of all pulmonary arterial segments affected by thromboembolic vascular lesions. Inter-observer agreement was calculated for both modalities using the intraclass-correlation-coefficient (ICC). Based on consensus reading the inter-modality agreement (CACTcons vs. CTPAcons) was calculated using the ICC. Inter-observer agreement was excellent for central vascular lesions (ICC > 0.87) and the percentage of affected segments (ICC > 0.76) and good for the perceptibility of mosaic perfusion (ICC > 0.6) and attribution of the pattern of mosaic perfusion (ICC > 0.6) for both readers on CACT and CTPA. Inter-modality agreement was excellent for the perceptibility of mosaic perfusion (ICC = 1), the present perfusion pattern (ICC = 1) and central vascular lesions (ICC = 1). However, inter-modality agreement for the percentage of affected segments was fair (ICC = 0.50), with a greater proportion of identified affected segments on CACTcons. CACT demonstrates a high agreement with CTPA regarding the detection of mosaic perfusion. CACT detects a higher number of peripheral vascular lesions compared to CTPA.