Objective: We aimed to study short-term heart rate variability (HRV) in 113 apparently healthy children permanent residents of moderate alti- tudes, the effects of gender and altitude. Materials and Methods: Children were assigned into 3 groups according with altitude of residence: Group 1 - 1650 m/a/s/l (n=38), Group 2 - 1740 m/a/s/l (n=36) and Group 3 - 2030 m/a/s/l (n=39). All children underwent short-term electrocardiographic recordings with spectral analysis of HRV at rest and during standing. Statistical analysis was performed using multivariate ANOVA analysis. Results: Heart rate variability analysis showed significant increase in SDNN, high frequency and total powers in parallel with increase of the altitude of residence (p<0.0001, p<0.03 and p<0.01, respectively). The magnitude of the HRV response to posture did not differ between groups except index of sympathetic modulation, LFNU, which rose to a significantly lesser degree (F=3.45, p<0.03) in Group 3, as compared with Group 1 and 2. Girls had lower HRV as compared with boys. Conclusion: Thus, in apparently healthy children, residents of moderate altitudes, increase in altitude levels is accompanied by higher overall vari- ability and parasympathetic modulation of the sinus node and lower sympathetic response to posture. Heart rate variability in children, residents of moderate altitudes is also dependent of gender, resembling similar relationship in inhabitants of sea level.