The clinical diagnosis of acute pulmonary embolism (PE) in patients with acute exacerbation of chronic obstructive pulmonary disease (COPD) is often difficult due to the similarity in the presenting symptoms of the two conditions. The purpose of this study was to determine the prevalence of PE in patients with acute exacerbation of COPD. Forty-nine consecutive patients admitted to our medical center for acute exacerbation of COPD were investigated for PE (whether or not clinically suspected), following a standardized algorithm based on D-dimer testing and computed tomography pulmonary angiography (CTPA). PE was ruled out by a D-dimer value <500 μg/L in 20 (41 %) patients and by negative CTPA in 40 (82 %). PE was confirmed in 9 patients. The prevalence of PE was 18 %. One patient with normal D-dimer had PE. Presenting symptoms and signs were similar between patients who did and did not have PE. PE was detected in 18 % of COPD patients who were hospitalized for an acute exacerbation. This finding supports the systematic evaluation of PE in hospitalized COPD exacerbated patients.