The most common cause of pulmonary artery filling defects on computed tomography pulmonary angiography or magnetic resonance imaging is pulmonary thromboembolism, but not infrequently, the presentation of this finding lacks specificity. Given that the morbidity and mortality associated with pulmonary thromboembolism is high, proper diagnosis of the condition is essential. Unusual or more rarely encountered etiologies must be considered when clinical manifestations and imaging findings are inconsistent. With this review, our purpose is to describe possible causes of pulmonary arterial filling defects. We aim to provide clinicians with a comprehensive list of differential diagnoses to facilitate a measured approach to the assessment of pulmonary arterial filling defects on computed tomography pulmonary angiography or magnetic resonance imaging.