Sarcopenia has never been diagnosed based on site-specific muscle loss, and little is known about the relationship between site-specific muscle loss and metabolic syndrome (MetS) risk factors. To this end, this cross-sectional study aimed to investigate the relationship between site-specific muscle size and MetS risk factors. Subjects were 38 obese men and women aged 40-82 years. Total body fat and lean body mass were assessed by whole-body dual-energy X-ray absorptiometry (DXA) scan. Muscle thickness (MTH) was measured using B-mode ultrasound scanning in six body regions. Subjects were classified into general obesity (GO) and sarcopenic obesity (SO) groups using the threshold values of one standard deviation below the sex-specific means of either MTH or skeletal muscle index (SMI) measured by DXA. MetS risk score was acquired by standardizing and summing the following continuously distributed variables: visceral fat area, mean blood pressure, HbA1c, and serum triglyceride / high density lipoprotein cholesterol, to obtain the Z-score. Multiple regression analysis revealed that the MetS risk score was independently associated with abdominal MTH in all subjects, but not with MTH in other muscle regions, including the thigh. Although HbA1c and the number of MetS risk factors in the SO group were significantly higher than those in the GO group, there were no significant differences between GO and SO groups as defined by SMI. Ultrasound-derived abdominal MTH would allow a better assessment of sarcopenia in obese patients and can be used as an alternative to the conventionally-used SMI measured by DXA.