Pulmonary thromboembolism (PTE) is considered an uncommon disease in Japan and there are not any reported prospective studies on the incidence of PTE in Japan. The objective of the present study was to determine the number of patients with PTE per year in a prospective study using a questionnaire. Letters were sent to clinical departments in university schools of medicine or medical colleges, and to hospitals with more than 100 beds. The diagnosis of PTE was to be confirmed by (1) pulmonary artery stenosis or occlusion on pulmonary angiography, (2) mismatch of pulmonary perfusion scintigraphy and pulmonary ventilation scintigraphy, (3) changes on pulmonary perfusion scintigraphy performed twice, or (4) autopsy. The questionnaire elicited 2,341 replies (the withdrawal rate was 40.7%). In 231 hospitals, 237 patients were diagnosed definitely during the study period of 2 months from 1 August to 30 September 1996. From this it was estimated that there are 3,492 (95% confidence interval: 3,280-3,703) patients with PTE per year, which implies that the incidence is 28 persons per 1,000,000 people per year, confirming that PTE is rare in Japan.