Presence of high fever may cause confusion in differential diagnosis of pulmonary embolism (PE) versus pneumonia. The aim of this study is to investigate the diagnostic value of serum procalcitonin (PCT) in differential diagnosis of PE and community-acquired pneumonia (CAP). A total of 24 patients with proven PE and 22 patients with CAP were included in the study. The study population was subdivided as PE patients with fever (group 1, n = 8) and without fever (group 2, n = 16); and CAP (group 3, n = 22). Serum PCT and systemic inflammatory markers were measured at the initial diagnosis and the third day of the treatment. The relation of PCT level with the other systemic inflammatory markers was investigated in each measurement point. The initial mean serum PCT level in group 3 (2.24 +/- 0.99 ng/mL) was statistically higher than group 1 (0.48 +/- 0.77 ng/mL) and group 2 (0.14 +/- 0.17 ng/mL; P = .000,.000, respectively). Procalcitonin level at the initial (2.24 +/- 0.99 ng/mL) and the third day of treatment (0.92 +/- 0.62 ng/mL) in group 3 showed a statistically significant reduction (P = .000). There were no statistically significant reduction in PCT levels by anticoagulation in groups 1 and 2 (P = .262, .119, respectively). Other systemic inflammatory markers including interleukin 6 (IL-6), C-reactive protein (CRP), and tumor necrosis factor alpha (TNF-alpha) levels statistically significantly decreased with anticoagulant and antimicrobial therapy. This study suggested that serum PCT level may be valuable for differentiating PE patients with or without fever from patients with CAP.