Objective:The purposes of this study were to investigate heart rate variability(HRV) in patients with generalized anxiety disorder(GAD) compared with major depressive disorder in Korea. Methods:Fifty-six GAD patients(20 male and 36 female) was classified into their comorbid psychiatric illness. Among them, Twenty-five patients(10 male and 15 female) who do not have any psychiatric comorbidity were compared with 30 major depressive disorder patients(12 male and 18 female). Clinical symptoms, HRV and MMPI were analysed between two group. Results:Comorbid psychiatric illnesses of GAD were ranked into no diagnosis(44.6%), MDD(32.1%), panic disorder(10.7%), social phobia(5.3%), PTSD(1.7%), OCD(1.7%), MDD+panic disorder(1.7%) and MDD+specific phobia(1.7%). GAD patients showed low functioning in HRV, but degree of decreasing HRV is not so severe compared with MDD patient. Balance of sympathetic and parasympathetic nerve tone is more severely impaired in GAD patients compared with MDD patient. The score of MMPI did not reveal any differences between two groups. Conclusions:The result showed that HRV can differenciate GAD and MDD patients. GAD patients could show decreased HRV functioning, less than MDD patients. But autonomic imbalance could be more severe in GAD than MDD patients.