PURPOSE: To examine which body position and indices present better reliability of heart rate variability (HRV) measures in children and to compare the HRV analyzed in different body positions between sexes. METHOD: Twenty eutrophic prepubertal children of each sex participated in the study. The RR intervals were recorded using a portable heart rate monitor twice a day for 7 min in the supine, sitting, and standing positions. The reproducibility was analyzed using the intraclass correlation coefficient (ICC; two way mixed) and within-subject coefficient of variation (CV).Two-way ANOVA with repeated measures was used to compare the sexes. RESULTS: High levels of reproducibility were indicated by higher ICC in the root-mean-square difference of successive normal RR intervals (RMSSD: 0.93 and 0.94) and Poincare plot of the short-term RR interval variability (SD1: 0.92 and 0.94) parameters for boys and girls, respectively, in the supine position. The ICCs were lower in the sitting and standing positions for all HRV indices. In addition, the girls presented significantly higher values than the boys for SDNN and absolute high frequency (HF; p < .05) in the supine position. CONCLUSIONS: The supine position is the most reproducible for the HRV indices in both sexes, especially the vagal related indices.