The significance of atherosclerotic calcified lesions observed on low-dose computed tomography (LDCT) performed during general checkups was investigated. The coronary arteries (CA), ascending aorta and aortic arch (AAAA), descending thoracic aorta (DTA), and abdominal aorta (AA) were examined. Semiquantitative calcified index analysis of the DTA and AA in terms of atherosclerosis risk factors and cardio-ankle vascular index (CAVI) measurements was also performed. We included 1594 participants (mean age: 59.2 years; range: 31-91 years). The prevalence of calcified lesions was 71.0%, 66.6%, 57.2%, and 37.9% in the AA, CA, AAAA, and DTA, respectively. Age-related advances in calcification among participants with no major risk factors, revealed that calcification appeared earliest in the AA, followed by the CA, AAAA, and DTA. Participants with calcified lesions in all arteries had a significantly greater CAVI than those without calcification. The CAVI was negatively correlated with low-density lipoprotein cholesterol levels, particularly in participants without calcified lesions in the DTA. Calcified lesions on LDCT could indicate the end stage of atherosclerotic lesions. The CAVI can be used to assess atherosclerotic changes at all stages of disease progression. A combination of LDCT and CAVI could be used as a routine non-invasive assessment of atherosclerosis.