Objective To evaluate the relation of coronary artery calcifications (CAC) on non-ECG-gated CT pulmonary angiography (CTPA) with short-term mortality in patients with acute pulmonary embolism (PE). Methods We retrospectively included all in-patients between May 2007 and December 2014 with an ICD-9 code for acute PE and CTPA and transthoracic echocardiography available. CAC was qualitatively graded as absent, mild, moderate, or severe. Relations of CAC with overall and PE-related 30-day mortality were assessed using logistic regression analyses. The independence of those relations was assessed using a nested approach, first adjusting for age and gender, then for RV strain, peak troponin T, and cardiovascular risk factors for an overall model. Results Four hundred seventy-nine patients were included (63 ± 16 years, 52.8% women, 47.2% men). In total, 253 (52.8%) had CAC—mild: 143 (29.9%); moderate: 89 (18.6%); severe: 21 (4.4%). Overall mortality was 8.8% ( n = 42) with higher mortality with any CAC (12.6% vs. 4.4% without; odds ratio OR 3.1 95%CI 2.1–14.5; p = 0.002). Mortality with severe (19.0%; OR 5.1 95%CI 1.4–17.9; p = 0.011), moderate (11.2%; OR 2.7 95%CI 1.1–6.8; p = 0.031), and mild CAC (12.6%; OR 3.1 95%CI 1.4–6.9; p = 0.006) was higher than without. OR adjusted for age and gender was 2.7 (95%CI 1.0–7.1; p = 0.050) and 2.6 (95%CI 0.9–7.1; p = 0.069) for the overall model. PE-related mortality was 4.0% ( n = 19) with higher mortality with any CAC (5.9% vs. 1.8% without; OR 3.5 95%CI 1.1–10.7; p = 0.028). PE-related mortality with severe CAC was 9.5% (OR 5.8 95%CI 1.0–34.0; p = 0.049), with moderate CAC 6.7% (OR 4.0 95%CI 1.1–14.6; p = 0.033), and with mild 4.9% (OR 2.9 95%CI 0.8–9.9; p = 0.099). OR adjusted for age and gender was 4.2 (95%CI 0.9–20.7; p = 0.074) and 3.4 (95%CI 0.7–17.4; p = 0.141) for the overall model. Patients with sub-massive PE showed similar results. Conclusion CAC is frequent in acute PE patients and associated with short-term mortality. Visual assessment of CAC may serve as an easy, readily available tool for early risk stratification in those patients. Key Points • Coronary artery calcification assessed on computed tomography pulmonary angiography is frequent in patients with acute pulmonary embolism. • Coronary artery calcification assessed on computed tomography pulmonary angiography is associated with 30-day overall and PE-related mortality in patients with acute pulmonary embolism. • Coronary artery calcification assessed on computed tomography pulmonary angiography may serve as an additional, easy readily available tool for early risk stratification in those patients.