Medical students are always confronted with significant stressors because of their course, hectic schedule, and enormous syllabus, which may affect their cardiac function and well being. A few studies have assessed cardiac autonomic modulation and correlated it with stress level in healthy medical students. We aimed to compare cardiac autonomic modulation and stress level between male and female medical students and correlate their stress levels with their cardiac autonomic modulation. The study was conducted on 15 healthy male (age 22.2±1.2 years) and 15 female (age 21.0±0.7 years) third year medical students. Their cardiac autonomic modulation was assessed using short-term heart rate variability (HRV) and stress scores were evaluated using medical student stressor questionnaire (MSSQ) which included parameters: academic related stressors, inter and interpersonal related stressors, teaching and learning related stressors (TLRS), drive and desire related stressors and social related stressors (SRS). Data were analyzed statistically. A P<0.05 considered statistical significant. Results showed mild to moderate levels of stress in all stressor parameters both in male and female students. There were no significant differences in stress scores between the groups. Markers of sympathetic actvity; LFnu and LF/HF ratio [1.1 (0.8-1.5) vs 0.4 (0.3-0.9), P= 0.007] were higher in male students, whereas, markers of parasympathetic activity; HFnu [46.7 (39.65- 55.9) vs 69 (52.85-75.3), P=0.01], HFpower, RMSSD, pNN50 [28.6 (6.65-39.85) vs 47.4 (26.45-55.85), P= 0.023] were higher in female students. HF power showed negative correlation with TLRS and SRS in male students, whereas, in female students none of the HRV variables showed correlation with stress scores. In the conclusion, similar mild to moderate levels of stress in all the stressor parameters were found in both male and female medical students. However, sympathetic activity was found more in male students, and parasympathetic activity more in female students. Parasympathetic activity was found decreased with increase in teaching and learning related stressors, and social related stressors in male students, whereas, in female students none of the HRV variables showed correlation with stresses scores. It indicates that cardiac autonomic modulation is not affected much with increase in stress level in female medical students. Key words: Stress, MSSQ, autonomic, heart rate variability, medical students