Background:The autonomic nervous system (ANS) is a complex network of nerves and ganglia that regulates involuntary functions of the body, including heart rate, blood pressure, digestion, respiratory rate, and glandular secretion. The present study was conducted to assess cardiac autonomous activity of malnourished and healthy children. Materials & Methods:45 malnourished (Group I) and 45 healthy children (Group II) of both genders were selected. Anthropometry, basal heart rate (BHR), blood pressure was determined. Time domain and frequency domain indices of HRV were assessed using RMS Polyrite D. Results: In group I and group II, body weight (kg) was 15.4 and 28.2, mean height (cm) was 106.3 and 120.4, MAC (cm) was 14.2 and 19.5, BMI (kg/m2) was 13.8 and 17.2, BHR (per min) was 87.4 and 84.2, systolic BP (mmHg) was 98.4 and 99.2 and diastolic BP (mm Hg) was 65.2 and 68.2 respectively. The difference was significant (P< 0.05).SDNN (ms) was 117.5 and 124.9, RMSSD (ms) was 59.5 and 52.3, pNN50 (%) was 34.8 and 28.5, LF (nu) was 47.4 and 32.9, HF (nu) was 53.8 and 65.2 and LF-HF ratio was 0.98 and 0.62 in group I and group II respectively. The difference was significant (P< 0.05). Conclusion: Children suffering from mild to severe malnutrition may experience decreased cardiac autonomic nerve function, which is characterized by sympathetic overactivity. MAC outperformed BMI as an HRV correlate.