BACKGROUND: Arrhythmia during coronary computed tomography angiography (coronary CTA) acquisition increases the risk of nondiagnostic segments and high radiation exposure. An advanced arrhythmia rejection algorithm for prospectively electrocardiogram (ECG)-triggered axial scans using dual-source CT (DSCT) examinations has recently been reported. OBJECTIVE: We compared image quality and effective dose at DSCT examinations using prospectively ECG-triggered axial scanning with advanced arrhythmia rejection software (PT-AAR) versus retrospectively ECG-gated helical scanning with tube-current modulation (RG-TCM) during arrhythmia. METHODS: This was a retrospective case-control study of 90 patients (43 PT-AAR, 47 RG-TCM) with arrhythmia (defined as heart rate variability [HRV] > 10 beats/min during data acquisition) referred for physician-supervised coronary CTA between April 2010 and September 2011. A subset of 22 cases matched for body mass index, HR, HRV, and other scan parameters was identified. Subjective image quality (4-point scale) and effective dose (dose length product method) were compared. RESULTS: PT-AAR was associated with lower effective dose than RG-TCM (4.1 vs 12.6 mSv entire cohort and 4.3 vs 9.1 mSv matched controls; both P < 0.01). Image quality scores were excellent in both groups (3.9 PT-AAR vs 3.6 RG-TCM) and nondiagnostic segment rates were low (0.1% vs 0.6%). Significantly higher image quality scores were found with PT-AAR in the entire cohort (P < 0.05), and in matched controls with high HRV > 28 beats/min (P < 0.05). CONCLUSIONS: In patients with variable heart rates, prospectively ECG-triggered axial DSCT with arrhythmia rejection algorithm is feasible and can decrease radiation exposure by approximately 50% versus retrospectively ECG-gated helical DSCT, with preserved image quality.