Background: Pulmonary embolism (PE) is thought to be associated with atrial fibrillation (AF). Nevertheless, this association is based on weak data. Objectives: To assess whether the presence of AF influences the clinical probability of PE in a cohort of patients with suspected PE and to confirm the association between PE and AF. Patients/Methods: We retrospectively analyzed the data from two trials that included 2'449 consecutive patients admitted for clinically suspected PE. ECG was systematically performed and PE was diagnosed by computer tomography. The prevalence of AF among patients with or without PE was compared in a multivariate logistic regression model. Results: The prevalence of PE was 22.8% (519/2'272) in patients without AF and 18.8% (25/133) in patients with AF (p=0.28). After adjustment for confounding factors, AF did not significantly modify the probability of PE (OR 0.68, 95%CI 0.42-1.11). However, when PE suspicion was based on new-onset dyspnea, AF significantly decreased the probability of PE (OR 0.47, 95%CI 0.26-0.84). If isolated chest pain without dyspnea was the presenting complaint, AF tended to increase the probability of PE (OR 2.42, 95%CI 0.97-6.07). Conclusions: Overall, the presence of AF does not increase the probability of PE when this diagnosis is suspected. Nevertheless, when PE suspicion is based on new-onset dyspnea, AF significantly decreases the probability of PE, as AF may mimic its clinical presentation. However, in patients with chest pain alone, AF tends to increase PE probability.