Heart rate variability (HRV) is affected by age, hyperglycemia and accumulation of body fat. This study compares the predictive value of four measurements of adiposity/obesity on HRV and investigates the specific role of age, metabolic contributors and degree/distribution of fat in HRV alterations. The sample consisted of 97 non-diabetic and non-medicated men with features of the metabolic syndrome (50+/-8 years of age, body mass index [BMI] 31+/-3 kg/m(2), waist circumference [WC] 107+/-9 cm, triglycerides 2.3+/-0.7 mmol/L, fasting glucose 6.0+/-0.5 mmol/L, insulin 156+/-71 pmol/L; mean+/-SD). WC, BMI, percent body fat (% fat, from dual energy X-ray absorptiometry) and visceral adipose tissue volume (VAT, from computed tomography) were used as measures of adiposity/obesity. HRV measures were obtained from 24-h, day- and night-time segments of Holter recordings. BMI presented no independent association with HRV. Percentage fat was the strongest obesity index to be associated with HRV: 24-h pNN50, rMSSD, HF and daytime pNN50, rMSSD, HF and LF (-0.27</=std beta</=-0.20, P<.05). VAT was associated with 24-h SDNN, LF (std beta=-0.25 and -0.20, P<.05, respectively) and daytime SDNN (std beta=-0.24, P<.05) while WC was associated with nighttime SDNN and SDANN (std beta=0.22 and 0.32, P<.05). In addition, age, fasting glucose, 2-h oral glucose tolerance test and triglycerides presented independent association with HRV. Adiposity/obesity measurements seem to be differently associated with HRV. An approach considering the combination of age, obesity and glucose metabolism factors could be helpful in the global cardiovascular risk management in abdominally obese men.