Background: The coronary artery calcification score (CACS) is a good marker of future cardiovascular risk. We determined the association between the CACS and the prognosis in patients who have undergone coronary computed tomography angiography (CCTA). Methods: We performed a prospective cohort study and enrolled 502 consecutive patients who underwent CCTA for screening of coronary artery disease (CAD) at Fukuoka University Hospital (FU-CCTA Registry) and either were clinically suspected of having CAD or had at least one cardiovascular risk factor with a follow-up of up to 5 years. The patients were divided into CACS = 0 and CACS > 0 groups. Using CCTA, ≥ 50% coronary stenosis was diagnosed as CAD, and the number of significantly stenosed coronary vessels (VD), Gensini score and CACS were quantified. The primary endpoint was major adverse cardiovascular events (MACE: cardiovascular death, ischemic stroke, acute myocardial infarction and coronary revascularization). Results: %CAD, the number of VD and the Gensini score in the CACS = 0 group were significantly lower than those in the CACS > 0 group. %MACE in the CACS = 0 group was also significantly lower than that in the CACS > 0 group. Kaplan-Meier curves indicated that the CACS = 0 group showed significantly greater freedom from MACE than the CACS > 0 group (P = 0.008). Finally, only CACS = 0 was independently associated with MACE (odd ratio: 0.41, 95% confidence interval: 0.17-0.97, P = 0.041). Conclusions: A CACS of 0 in patients who underwent CCTA was associated with a good prognosis.