Objective: To evaluate heart rate variability by Holter monitoring in type 1 diabetic children compared with a healthy control group and determine the factors modifying heart rate variability. Methods: This was designed as a prospective study comparing 28 patients, diagnosed with type 1 diabetes and under follow-up, with 27 healthy control group subjects. Results: The patients were aged 9.9 ± 4.2 years in the diabetic group, including 13 (46.5%) girls and 15 (53.5%) boys. The healthy control group comprised 20 (74%) girls and seven boys (26%) with an average age of 8.6 ± 3.7 years. The search for factors modifying heart rate variability yielded the following correlations: for the time-dependent variables, negative between age and both average and maximal heart rate (r = −0.263 and −0.460, respectively), negative between haemoglobin A1c and percentage of differences between adjacent RR intervals >50 ms, positive between diabetes duration and square root of the mean of the sum of squares of differences between adjacent NN intervals. The average heart rate and percentage of differences between adjacent RR intervals >50 ms was significantly higher in the girls than the boys in all groups. With regard to the frequency-dependent factors affecting heart rate variability, correlations were found between haemoglobin A1c level and both total power and very low frequency (r = −0.751 and −0.644) and between very low frequency and diabetes duration. Conclusion: A reduction in heart rate variability parameters was observed in type 1 diabetes mellitus patients who had a long disease duration or were poorly controlled, as compared with healthy controls.