Metabolic syndrome (MetS) is a cluster of metabolic conditions that aggravate the likelihood of cardiovascular diseases and type 2 diabetes mellitus. This study was aimed to identify the best obesity index to determine MetS. This was a cross-sectional study and part of the Ellisras Longitudinal Study where 593 (289 males and 304 females) adults aged 22–30 years took part. Confirmatory factor analysis was used to test the single-factor models of MetS defined by mid arterial pressure, fasting blood glucose, triglycerides and commonly selected obesity indices such as Neck circumference (NC), Body mass index (BMI), Waist circumference (WC) and Waist to height ratio (WHtR) as indicators of MetS. It was found that a single model fit built based on WC and WHtR suggested a better fit index than NC and BMI in males, whereas, a model built on NC obtained a better fit index for females than other factor models. In conclusion, the result of the present study suggests that in rural Ellisras adult’s, WC and WHtR are the best obesity indices for determining MetS in males and NC in females than other indices. Hence, longitudinal studies are recommended to allow causality to be drawn between obesity indices and MetS.