We aimed to evaluate image quality, radiation dose and diagnostic accuracy of coronary CT angiography (CCTA) with a prospectively gated transverse-axial scan (PGT) compared with a retrospectively gated helical scan (RGH), using a 64-slice scanner in patients who underwent coronary artery bypass graft (CABG). Of the 131 consecutive patients that underwent CABG using 64-slice multidetector row computed tomography during 2008, patients with heart rate (HR) of <75 beats/minute (bpm), and HR variation <10 bpm were included in the study. PGT was performed on 39 patients with 93 grafts, with RGH performed on 43 patients with 102 grafts. Image quality (1: excellent-4: poor) and estimated radiation dose were compared between the two groups. Of these, a total of 64 segments in 26 patients were subjected to invasive coronary angiography (ICA) for clinical reasons. Diagnostic accuracy of CCTA for evaluation of graft was performed between the two groups with ICA as a reference standard in terms of significant stenosis (≥ 50% of luminal stenosis). The image quality was not statistically different in the two groups. Mean effective radiation dose was 6.5 mSv in PGT-group, which was significantly lower than that in the RGH-group (21.2 mSv; P < 0.001). There was no statistically significant difference in diagnostic accuracy between the two groups (PGT-group versus RGH-group; 93.1% versus 91.4%). PGT can achieve dose reductions of up to 70% compared to RGH while maintaining image quality and high diagnostic accuracy in patients undergoing CABG.