Objective Diet exerts a crucial role on cardiovascular health. Evidence is mainly based on the content and the amount of dietary intakes. Some recent reports demonstrated that eating behaviour may also be of significant importance in cardiovascular health. In this study we aimed to investigate the effects of eating behaviour on heart rate variability (HRV) in healthy subjects.Methods and results In total, 521 healthy subjects with 24-hour Holter ECG recordings filled out a special questionnaire about their eating behaviour and lifestyles. From these patients, 425 subjects were healthy and had recordings suitable for analysis. Five types of eating behaviour were assessed in the questionnaire: (1) adherence to the Mediterranean diet (using the MedDietScore), (2) skipping breakfast, (3) late night eating, (4) having snacks, and (5) rapid eating. Physical exercise level and active working status of the subjects were also assessed. The root mean square of successive differences (RMSSD) was used for assessment of HRV.RMSSD values were lower in subjects skipping breakfast compared to subjects having breakfast regularly (26.32 vs 31.52 P = 0.02). Other behavioural patterns did not have any effect on the HRV parameters. Ageing, male sex, sedentary lifestyle and no active working were also found to be associated with reduced HRV in univariate analysis. In multivariate regression analysis, age and skipping breakfast were the only parameters significantly associated with a lower RMSSD (β: –0.222, P: 0.008 and β: –0.191, P: 0.020, respectively)Conclusions The findings of this study showed that skipping breakfast may be a cause of cardiac autonomic dysfunction.