Dietary fish oil supplementation and regular physical activity can improve outcomes in patients with established CVD. Exercise has been shown to improve heart rate variability (HRV), a predictor of cardiac death, but whether fish oil benefits HRV is controversial. Obese adults at risk of future coronary disease have impaired HRV and may benefit from these interventions. We evaluated the effect of DHA-rich tuna fish oil supplementation with and without regular exercise on HRV in sedentary, overweight adults with risk factors for coronary disease. In a randomised, double-blind, parallel comparison, sixty-five volunteers consumed 6 g fish oil/d (DHA 1.56 g/d, EPA 0.36 g/d) or sunflower-seed oil (placebo) for 12 weeks. Half of each oil group also undertook regular moderate physical activity (3 d/week for 45 min, at 75 % of age-predicted maximal heart rate (HR)). Resting HR and the HR response to submaximal exercise were measured at weeks 0, 6 and 12. In forty-six subjects, HRV was also assessed by power spectrum analysis of 20 min electrocardiogram recordings taken supine at baseline and 12 weeks. Fish oil supplementation improved HRV by increasing high-frequency power, representing parasympathetic activity, compared with placebo (P = 0.01; oil x time interaction). It also reduced HR at rest and during submaximal exercise (P = 0.008; oil x time interaction). There were no significant fish oil x exercise interactions. Dietary supplementation with DHA-rich fish oil reduced HR and modulated HRV in keeping with an improved parasympathetic-sympathetic balance in overweight adults with risk factors for future coronary disease.