Purpose: The aim of the present study was to investigate the association between plasma homocysteine (Hcy) levels and carotid, cardiac, and renal end-organ damage in newly diagnosed type 2 diabetes mellitus (T2DM) patients. Methods: Newly diagnosed normotensive T2DM patients (n = 390) were enrolled in this study. The patients were not taking any medications over the duration of the study. The left ventricular mass index (LVMI), carotid intima media thickness (CIMT), and creatinine levels and 24-h microalbuminuria were used to determine cardiac, carotid, and kidney end-organ diseases, respectively. Results: Using univariate logistic regression analysis; age, 24-h microalbuminuria, fasting blood glucose, CIMT, creatinine level, and LVMI were found to be significantly associated with the Hcy level. When those six variables were included in a multivariate regression model, CIMT, LVMI, and creatinine were found to be significantly associated with the Hcy level. We determined that an Hcy level >12.5 mu mol/L was predictive of high LVMI, with a sensitivity of 70.1% and a specificity of 68%. An Hcy level >13.5 mu mol/L was predictive of high CIMT, with a sensitivity of 67.5% and a specificity of 63.1%. Conclusion: In this study, LVMI, CIMT, and creatinine level were positively correlated with the Hcy level. We believe that the Hcy level may be a useful predictor of end-organ damage, including cardiac, carotid, and renal diseases, in newly diagnosed T2DM patients.