Background: To evaluate the prognosis after pulmonary thromboendarterectomy (PTE) in patients with chronic thromboembolic pulmonary hypertension (CTEPH), a lung biopsy was performed in 34 patients with central CTEPH and in 7 patients with peripheral CTEPH during PTE. Methods and Results: Postoperative prognosis was classified from A to E based on the postoperative hemodynamic parameters and clinical condition, and was compared with the index of occlusion (IOCTEPH), which indicates the degree of occlusion in the small pulmonary arteries. Criteria of (A–E) were established only for central CTEPH. Category (A) corresponded to an IOCTEPH from 1.0 to 1.4, (B) from 1.5 to 1.7, (C) from 1.8 to 2.0, and (D) from 2.1 to 2.4. One patient with an index of 3.0 was rated as (E). This patient had collateral vessels around the obstructed small pulmonary arteries and died postoperatively. In all 12 patients who underwent PTE after the criteria were established, postoperative hemodynamic parameters and clinical conditions were consistent with the IOCTEPH. One patient with a high degree of medial atrophy in their small pulmonary arteries died after PTE. Conclusions: These results indicate that a lung biopsy during PTE is useful for prognostication in patients with CTEPH.  (Circ J 2014; 78: 476–482)