This study aimed to evaluate the most valid index among various indices of low muscle mass in assessing cardiometabolic risks in a Korean population. Appendicular lean mass index (ALMI, kg/m2), fat mass index (FMI, kg/m2), FMI-adjusted ALMI (ALMfmi), ratio of ALM to weight index (ALMwt), ratio of ALM to body mass index (ALMbmi) and ratio of ALM to truncal fat index (ALMtrunkfat) were measured by dual energy X-ray absorptiometry in 17,870 participants from 2008 to 2011. We adopted all the aforementioned indices of low muscle mass expressed as sex- and age-specific standard deviation scores (Z-scores). Low muscle mass for age was defined as Z-score <-1. The prevalence of low muscle mass was approximately 16% across all indices. Low muscle mass defined by ALMI had low muscle mass and low fat mass, and ALMfmi had low muscle mass at the same FMI. However, low muscle mass defined by ALMwt, ALMbmi and ALMtrunkfat had similar muscle mass with high FMI. The receiver operating characteristic curve in metabolic syndrome showed that the ALMtrunkfat was 0.74 in male and 0.69 in female, indicating that ALMtrunkfat was the best discrimination index for metabolic syndrome. This study showed that ALMtrunkfat could be a useful indicator for screening cardiometabolic risk factors, particularly in normal or overweight Asian population.