Introduction: Generalised anxiety disorder (GAD) is known to affect autonomic nervous system though the studies showing gender based effect are conflicting. We conducted this study to compare the effect of GAD on the basis of gender. Material and Method: 60 GAD patients were divided into 2 groups of 30 each. Group I comprised of 30 male patients and group II of 30 female patients. Basal heart rate and RR intervals were compared among the two groups. Conclusion: Significant increase in heart rate and highly significant decrease in RR interval among female GAD patients compared to male GAD patients