The purpose of the study was to evaluate the prevalence of atelectasis as an alternative diagnosis in patients who underwent computed tomographic pulmonary angiography (CT-PA) for suspected pulmonary embolism (PE), and to contrast the pathophysiology of pulmonary atelectasis and PE, both of which are associated with dyspnea and hypoxemia. We retrospectively identified 144 consecutive emergency department patients (n=49) and inpatients (n=95) admitted between July 2001 and June 2002 who were evaluated with CT-PA for suspected PE. There were 98 women and 46 men with a mean age of 58 years (range 27-95 years). Each CT report was reviewed for PE, the words "atelectasis," "collapse," and/or "volume loss," findings known to predispose to atelectasis, and alternative diagnoses. CT scans of those with PE and those with atelectasis were reviewed. Each case was categorized into one of three groups, as follows: group 1, PE; group 2, atelectasis of three or more segments and no PE; group 3, neither PE nor atelectasis. PaO2 was documented, when available (n=115), with PaO2 >100 mmHg recorded as 100 mmHg. Reports for group 3 were reviewed for alternative diagnoses. Thirteen percent of the study population (19/144, group 1) had PE, and two of them had concomitant atelectasis; mean PaO2 was 69 mmHg (range 38-100 mmHg). Nineteen percent of the study population (27/144, group 2) had atelectasis of three or more segments without PE; mean PaO2 was 73 mmHg (range 45-100 mmHg). Sixty-eight percent of the study population (98/144, group 3) had neither PE nor atelectasis; mean PaO2 was 79 mmHg (range 36-100 mmHg). There was a significant difference in the PaO2 between groups 1 and 3 (Student's t-test), with group 2 intermediate. Seventy percent of group 2 (19/27) had at least one finding predisposing to atelectasis: central bronchial abnormality (n=6), moderate or larger pleural effusion (n=11), pleural mass, pneumothorax, elevated hemidiaphragm, and severe kyphosis (the last four all n=1 each), versus 16% (3/19) of group 1 ( P<0.05). Sixty-three percent of group 3 (62/98) had one or more alternative diagnoses on CT that explained the patient's symptoms as follows: pneumonia (28%, 27/98), other lung disease (18%, 18/98), congestive heart failure (13%, 13/98), and malignancy (13%, 13/98). Pulmonary atelectasis was common in patients undergoing CT-PA for suspected PE, equaling pneumonia as the most common alternative diagnosis. Most patients with atelectasis had predisposing findings on CT. Pulmonary atelectasis and PE cause similar symptoms by different mechanisms of ventilation-perfusion mismatch.