The purpose of this study was to examine differences in heart rate variability (HRV) in metabolic syndrome (MetS) and to determine associations between HRV parameters, MetS risk factors, and insulin resistance (homeostasis model assessment for insulin resistance (HOMA-IR)). Participants (n = 220; aged 23-70 years) were assessed for MetS risk factors (waist circumference, blood pressure, fasting plasma glucose, triglycerides, and high-density lipoprotein cholesterol) and 5-min supine HRV (time and frequency domain and nonlinear). HRV was compared between those with 3 or more (MetS+) and those with 2 or fewer MetS risk factors (MetS-). Multiple linear regression models were built for each HRV parameter to investigate associations with MetS risk factors and HOMA-IR. Data with normal distribution are presented as means +/- SD and those without as median [interquartile range]. In women, standard deviation of R-R intervals 38.0 [27.0] ms, 44.5 [29.3] ms; p = 0.020), low-frequency power (5.73 +/- 1.06 ln ms(2), 6.13 +/- 1.05 ln ms(2); p = 0.022), and the standard deviation of the length of the Poincare plot (46.8 [31.6] ms, 58.4 [29.9] ms; p = 0.014) were lower and heart rate was higher (68 [13] beats/min, 64 [12] beats/min; p = 0. 018) in MetS+ compared with MetS-, with no differences in men. Waist circumference was most commonly associated with HRV, especially frequency domain parameters. HOMA-IR was associated with heart rate. In conclusion, MetS+ women had a less favourable HRV profile than MetS- women, but there were no differences in men. HOMA-IR was associated with heart rate, not HRV.