The objective of this study was to determine quantitative and qualitative surfactant alterations, proteins, and platelet activating factor (PAF) in bronchoalveolar lavage (BAL) fluid from patients with pulmonary thromboembolism (PTE) with respect to ventilated patients without PTE. Patients with PTE underwent BAL at the most affected lung area on the first and tenth days of PTE diagnosis. Total proteins and albumin, total lipids, individual phospholipid classes, PAF and PAF-acetylhydrolase (PAF-AcH) activity were determined in BAL fluid. Total proteins and albumin were found to be increased in both successive samples of patients with PTE when compared with the control group (p < 0.001 and p < 0.05, respectively). Total phospholipids, though, were elevated on the first day, but they decreased on the tenth day, in comparison with the control groups (p < 0.05). Alterations in the percentage of individual phospholipid classes were observed in both successive samples of BAL fluid when compared with those in the control subjects. PAF and PAF-AcH were detected in high levels on the first day (p < 0.001), which were reduced on the tenth day (p < 0.05). An inverse correlation between PAF levels and PaO2/FiO2 ratio was observed. Finally, the percentage of macrophages decreased and the percentage of neutrophils increased during the course of PTE. In conclusion, pulmonary embolism is associated with alterations in lung surfactant and inflammation in lung tissue, expressed by an increase in PAF and in neutrophils.