Objective To explore the differences in heart rate variability(HRV)between patients with bipolar disorder(BD)and generalized anxiety disorder(GAD).Methods A total of 57 patients with BD(BD group)and 60 patients with GAD(GAD group)were selected and tested for HRV,and their HRV-related indicators SDNN-24(24 h-standard diviation of NN intervals),SDNN(standard deviation of NN intervals),SDANN(standard deviation of average NN intervals in all 5 min segments of the entire recording),rMSSD(root mean square difference between adjacent R-R intervals),PNN50(percentage of difference between adjacent R-R intervals>50 ms),TP(total power),LF(low-frequency power),HF(high-frequency power),and the ratio between LF and HF(LF/HF)were compared.Results The disease course of GAD group was shorter than that of BD group(P<0.01).The indicators of SDNN-24 and SDANN in GAD group were lower than those in BD group(P<0.01).Correlation analysis showed that the disease course was negatively correlated with TP,LF,HF and SDNN in GAD group(P<0.05).Conclusion The somatoform autonomic dysfunction of GAD patients is more serious than that of BD patients.The disease course of GAD patients can affect their HRV indicators.