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Background Atrial fibrillation ( AF ) is a well‐established risk factor for ischemic stroke ( IS ). Emerging evidence also indicates an association between AF and pulmonary embolism ( PE ). Because IS may potentially mediate the observed risk of PE in AF , we aimed to assess the impact of AF on the cause‐specific risks of PE and IS in a large cohort recruited from the general population. Methods and Results We observed 29 842 participants from 3 surveys of the Tromsø study (inclusion in 1994–1995, 2001–2002, and 2007–2008) to the end of 2012. Incident events of AF , IS, and PE during follow‐up were recorded, and information on potential confounders was obtained at baseline. Cox regression models, with AF as a time‐dependent variable, were used to calculate cause‐specific hazard ratios ( HR s) with 95% confidence intervals ( CI s) for PE and IS . There were 2067 participants diagnosed as having AF , 296 with PE and 1164 with IS, during a median of 17.6 years of follow‐up. The risks of PE ( HR, 10.88; 95% CI , 6.23–18.89) and IS ( HR, 6.16; 95% CI , 4.47–8.48) were substantially increased during the first 6 months after AF diagnosis, with crude incidence rates of 18.5 per 1000 person‐years for PE and 52.8 per 1000 person‐years for IS . The risk estimates remained elevated for both PE ( HR , 1.72; 95% CI, 1.10–2.71) and IS ( HR, 2.45; 95% CI, 2.05–2.92) throughout the study period. Conclusions AF was associated with increased cause‐specific risks of both PE and IS . Our findings infer that the risk of PE in AF is not explained by intermediate IS .