We aimed to investigate the prevalence and severity of noncalcified coronary plaques (NCP) using coronary CT angiography (CCTA) and analyze predictors of significant coronary stenosis by NCP in asymptomatic subjects with low coronary artery calcium score (CACS). The institutional review board approved this retrospective study and all patients gave written, informed consent. The presence of plaque, severity of stenosis, plaque characteristics, and CACS were assessed in 7,515 asymptomatic subjects. We evaluated the prevalence and severity of NCP in subjects having low CACS (707 subjects; men with CACS from 1 to 50 and women from 1 to 10) in comparison to those having 0 CACS (6,040 subjects) as the reference standard. Conventional risk factors were assessed for predictors of NCP and significant stenosis by NCP. We also investigated the cardiac events of the patients through medical records. Compared to subjects with 0 CACS, those with low CACS showed higher prevalence of NCP (6.9% vs. 31.5%, P < 0.001) and significant stenosis caused by NCP (0.8% vs. 7.5%, P < 0.001). In the low CACS group, independent predictors for significant NCP included diabetes mellitus (DM), hypertension, and elevated low-density lipoprotein (LDL)-cholesterol (all P < 0.05). However, 47.2% of subjects with significant NCP were classified into the low to intermediate risk according to Framingham Risk Score. At the median follow up of 42 months (range: 3–60 months), cardiac events were significantly higher in the low CACS group compared to the 0 CACS group (2.6% vs. 0.27%, P < 0.001). In asymptomatic subjects having low CACS, the prevalence and severity of NCP were higher as compared to subjects having zero CACS and predictors of significant stenosis by NCP were DM, hypertension and LDL-Cholesterol. Therefore, CCTA may be useful for risk stratification of coronary artery disease as added value over CACS in selected populations with low CACS who have predictors of significant NCP.