High reproducibility on coronary artery calcium scoring is a key requirement in monitoring the progression of coronary atherosclerosis. The purpose of this prospective study is to assess the reproducibility of 1.25-mm- and 2.5-mm-thickness images on prospective electrocardiograph-triggered 64-slice CT with respect to 2.5-mm-thickness images on spiral overlapping reconstruction. One hundred patients suspected of coronary artery disease were scanned twice repeatedly, both on prospective electrocardiograph-triggered step-and-shoot and retrospective electrocardiograph-gated spiral scans. Using 1.25-mm-thickness collimation, 1.25-mm- and 2.5-mm-thickness image sets on prospective scans and 2.5-mm-thickness image sets with 1.25-mm increment (overlapping) on retrospective scans were obtained. Coronary artery calcium scores, interscan variability and interobserver variability were evaluated. The mean interscan variability in coronary artery calcium measurement on 1.25-mm prospective/2.5-mm prospective/2.5-mm overlapping retrospective scans were Agatston: 10%/18%/12%, volume: 10%/12%/10% and mass: 8%/13%/11% for observer 1 and Agatston: 8%/14%/10%, volume: 7%/9%/10% and mass: 7%/10%/9% for observer 2, respectively. The mean interobserver variability was 5% to 14%. In conclusion, prospective electrocardiograph-triggered 64-slice CT using the 1.25-mm prospective scan shows the lowest variability. The 2.5-mm prospective scan on volume or mass scoring shows variability of around 10%, comparable to 2.5-mm-thickness spiral overlapping reconstruction images.