This paper provides age- and sex-specific reference values for short-term heart rate variability (HRV) data in children by time domain and frequency domain methods. Furthermore, HRV determinants will be determined. In 460 children (5-10 years), 5-minute HRV measurements in supine position were undertaken with Polar chest belts. The data were manually edited and processed with time and frequency domain methods. Age, time point, physical activity (accelerometry), physical fitness (cardiopulmonary fitness, upper and lower limb muscular fitness) and body composition (body mass index, fat%, fat and fat-free mass) were analysed as determinants using multiple regression analysis stratified by sex. Sex- and age-specific reference values were produced. Overall, girls had lower HRV. Age-related parasympathetic increases and sympathetic decreases were seen with sometimes age-related year-to-year wave-like changes in boys. The time point of recording had limited influence on HRV. Of the lifestyle related factors, fatness (only 7 % overweight) was not associated with HRV but fat-free mass, physical activity and in particular physical fitness (over and above activity) had a favourable association by increased parasympathetic activity. Future HRV studies in children should consider age, sex and physical fitness.