We performed a prospective study to determine the evolution of perfusion defects 6 months after pulmonary thromboembolism (PTE), to identify associated factors and to evaluate the incidence of subclinical recurrence. Seventy patients diagnosed of PTE were enrolled. Perfusion pulmonary scintiscans were performed 6 months after the acute PTE episode and the results were compared with initial defects. We looked for significant relations between several course profiles and factors such as age, sex, anticoagulation therapy and patient history. Defects revealed by the initial scintiscan remained the same 6 months later in 15 (21%), decreased in 35 (53%) and disappeared in 16 (23%) of the 70 patients. New defects were identified in 2 patients. A significant relation was found between a favorable outcome as shown by follow-up scintiscans and compliance with anticoagulation therapy (p = 0.0024). Other statistically significant relations were observed between favorable outcome and a history of surgical intervention during the acute episode (p = 0.004) and between unfavorable outcome and a history of venous thromboembolic disease (p = 0.004).