Cardiovascular disease is a major cause of morbidity and mortality in type 2 diabetic (T2DM) patients. Low levels of high-density lipoprotein cholesterol (HDL-C) is the commonest lipid abnormality in Nigerian T2DM patients. The association of HDL-C subfractions (HDL-2 and HDL-3) and the presence of coronary artery disease (CAD) is still unknown among Nigerian T2DM patients. Asymptomatic T2DM patients attending the diabetes clinic of the Nnamdi Azikiwe University Teaching Hospital, Nnewi, Nigeria were identified and recruited for this study. History, physical examination and clinical evaluations were done for study participants. Data obtained were verified and analyzed with appropriate software. Tests for normality were done and comparison of variables in participants with and without CAD done with statistical tests appropriate for non-parametric data. Logistic regression analysis was used to determine the odds at which independent risk factors predicted coronary artery disease. Four hundred study participants consisting of 174 (43.5%) males and 226 (56.5%) females participated in this study. The median (IQR) age of participants was 60(48,65) years. 64(16%) participants had coronary artery disease. The HDL-3 subfraction of HDL-C was significantly lower in those with CAD (Mann-Whiney U=254, p=0.02) with OR=4.6 (95%CI=3.2-7.9, p=0.01) after replacement of significant predictors of CAD in the logistic regression model. There was no significant difference in HDL-2 levels in subjects with CAD compared to those without CAD (Mann-Whitney U=21, p=0.21). The HDL-3 phenotype of HDL-C is a significant predictor of CAD in Nigerian T2DM patients.