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The management of chronic thromboembolic pulmonary hypertension (CTEPH) is dependent on the extent of pulmonary artery obstruction, which is usually evaluated by planar perfusion scanning and CT pulmonary angiography (CTPA). We previously reported that SPECT perfusion scanning is more sensitive than planar scanning for detecting vascular obstruction in CTEPH. The purpose of this study is to compare SPECT with CTPA for detecting segmental pulmonary artery obstruction in CTEPH.SPECT and CTPA were carried out before pulmonary endarterectomy in 12 CTEPH patients. Field experts documented the anatomical distribution of perfusion defects disclosed by SPECT, the anatomical distribution of pulmonary arterial filling defects disclosed by CTPA and the segmental anatomy of the vascular obstructions based on a review of clinical and pathology records, without knowledge of scan results.Clinical/pathological evaluation disclosed 140 obstructed (15.5 ± 2.5 per patient) and 40 unobstructed lung segments. SPECT scanning identified 87/140 (62%) of the obstructed and 29/40 (72%) of the unobstructed segments. By comparison, CTPA identified 67/140 (47.8%) of the obstructed and 32/40 (80%) of the unobstructed segments. Sensitivity for detecting obstructed segments was significantly higher for SPECT compared with CTPA (62 ± 4.1% vs 47.8 ± 2.9%, respectively;P= 0.03).SPECT is more sensitive than CTPA for identifying obstructed segments in this small sample of CTEPH patients. However, even SPECT under-represents the extent of vascular obstruction from this disease.