Heart rate variability (HRV) is associated with an increased risk of cardiovascular morbidity and mortality. HRV is in part a function of the activity of the autonomic nervous system and has been associated with low-grade inflammation. In patients with type 2 diabetes, HRV is decreased and is a predictor of poor outcome. As HRV and its determinants in non-diabetic individuals have not been studied properly, the aim of this observational study was to evaluate possible associations between HRV vs. impaired fasting glucose, insulin resistance, lipidaemia and markers of inflammation and immune activation in these individuals. Healthy individuals (n = 596, 55-75 years) from the community were evaluated with ambulant 48-h continuous electrocardiogram monitoring and fasting markers of lipidaemia, inflammation and immune activation, respectively. Insulin resistance was estimated by HOMA-IR. Time domain components of HRV were calculated. Heart rate and HRV were not associated with glucose metabolic parameters but were inversely associated with soluble urokinase plasminogen activator receptor (suPAR), high-sensitive CRP and leucocyte number (P < 0·001), respectively. Both 24-h and night-time HRV were inversely associated with plasma triglyceride, whereas HDL, LDL and total cholesterol were not. A model including suPAR, CRP, gender, triglyceride, age, systolic blood pressure, physical activity and smoking status explained 12·2% (P < 0·0001) of the 24-h HRV and 7·3% (P < 0·0001) of the night-time HRV. The single strongest factor to explain 24-h and night-time HRV appeared to be suPAR (P = 0·001 and P = 0·0067, respectively). A low HRV is not related to prediabetes, that is, insulin resistance and impaired fasting glucose, but is related to the immune and inflammatory markers suPAR and CRP and plasma triglyceride.