Objective The aim of this study was to evaluate independent predictors for coronary artery stenosis in patients with type 2 diabetes mellitus (DM) and subclinical atherosclerosis. Methods A total of 232 patients with type 2 DM and subclinical atherosclerosis underwent multi-slice computed tomography coronary angiography (MSCTA). Subclinical atherosclerosis was determined by carotid intima-media thickness (IMT) or carotid plaque. Results MSCTA revealed significant coronary stenosis (>50% in diameter) in 71 subjects (31%). The subjects who had significant coronary stenosis were much older and had a longer duration of DM. In particular, the log-transformed albumin:creatinine ratio (ACR) was higher in the subjects with significant coronary stenosis when compared with the subjects without significant coronary stenosis. The age- and sex-adjusted odds ratio for significant coronary stenosis increased in proportion to albuminuria with a given estimated glomerular filtration rate. The ACR as a continuous variable (odds ratio 4.167, 95% CI = 1.497-11.599) or a categorical variable (ACR > 30 mg/mg, odds ratio 4.619, 95% CI = 1.562-13.659) was associated with increased risk of significant coronary stenosis, independent of conventional cardiovascular risk factors. In ROC analysis, ACR had an additive effect with carotid IMT for predicting significant coronary stenosis (AUC 0.625 with carotid IMT; AUC 0.710 with carotid IMT plus ACR, P = 0.0144). Conclusion In conclusion, the presence of albuminuria is an independent predictor for significant coronary stenosis in patients with type 2 DM and subclinical atherosclerosis.