As the influence of diet on health may take place over a period of decades, there is a need for biomarkers that help to identify those aspects of nutrition that have either a positive or a negative influence. The evidence is considered that heart-rate variability (HRV) (the time differences between one beat and the next) can be used to indicate the potential health benefits of food items. Reduced HRV is associated with the development of numerous conditions for example, diabetes, cardiovascular disease, inflammation, obesity and psychiatric disorders. Although more systematic research is required, various aspects of diet have been shown to benefit HRV acutely and in the longer term. Examples include a Mediterranean diet, omega-3 fatty acids, B-vitamins, probiotics, polyphenols and weight loss. Aspects of diet that are viewed as undesirable, for example high intakes of saturated or trans-fat and high glycaemic carbohydrates, have been found to reduce HRV. It is argued that the consistent relationship between HRV, health and morbidity supports the view that HRV has the potential to become a widely used biomarker when considering the influence of diet on mental and physical health.