The definition of Metabolic Syndrome (MS) required an ethnic-specific cut-off point for waist circumference (WC). We aim to assess the optimal ethnic-specific WC cut-off point for MS in Indonesia, a multi-ethnic country. Three population-based studies in Indonesia were included for analysis [Flores (n = 1227, Floresian), Depok (n = 904, Sundanese), and Jakarta (n = 1574, Javanese)]. All subjects were 25–65 years old. The receiver operator characteristic curve analysis and Youden index method was used to determine the optimal cut-offs of WC to predict two or more risk factors of MS. In Flores, the cut-offs were 80 cm (Sensitivity and Specificity, AUC, 84% and 73%, 0.86) and 77 cm (86% and 68%, 0.85), for men and women, respectively. While in Depok, the values were 87 cm (87% and 67%, 0.85) and 79 cm (94% and 54%, 0.79), for men and women, respectively. While in Jakarta, the values were 83 cm (92% and 60%, 0.85) and 81 cm (84% and 60%, 0.77), for men and women, respectively. The optimal WC cut-off values for MS were different in those three ethnicities, and in general were lower than the currently used cut-off points for Asian population.