BACKGROUND: Obesity causes changes in cardiac autonomic modulation. OBJECTIVE: To investigate the autonomic modulation of eutrophic and obese children by means of indexes of heart rate variability (HRV) obtained through geometric methods. METHODS: We analyzed data from 133 children aged 8 to 13, divided into two groups: obese (n = 61) and eutrophic (n = 72) according to body mass index for age and sex. For the analysis of HRV, heart rate was recorded beat-to-beat. The RR intervals were transformed into geometric figures, and from them, we calculated the triangular index (RRtri), triangular interpolation of RR intervals (TINN), the indexes SD1, SD2 and SD1/SD2 ratio, obtained from the Poincare plot. Visual analysis of the plot was also performed. Student\'s t test was performed for unpaired data and Mann-Whitney\'s test, with significance level of 5.0%, for data analysis. RESULTS: In obese children, RRtri indexes were proven to be reduced (0.0730 vs 0.1084 [median]), TINN (171.80 +/- 55.08 vs 218.26 +/- 51.12), SD1 (19.93 +/- 9.10 vs 24.10 +/- 8.03) and SD2 (51.63 +/- 16.53 vs 69.78 +/- 17.19). The SD1/SD2 ratio showed no significant differences (0.3781 +/- 0.12 vs 0.3467 +/- 0.08). Visual analysis of the plot, in obese children, revealed a smaller dispersion of RR intervals both beat-to-beat, and in the long term, indicating lower HRV. CONCLUSION: Obese children presented changes in the autonomic nervous system characterized by decreases in parasympathetic activity and overall variability.