We assessed HRV (heart rate variability) in 31 patients with panic disorder before and after 6-weeks treatment with antidepressants and CBT and 18 controls. Patients were regularly assessed weekly on the CGI, BAI and BDI. HRV was assessed during 3 positions. Thirty one pharmacoresistant panic disorder patients entered a 6-week open-label treatment study. A combination of CBT and pharmacotherapy proved to be the effective treatment. Patients significantly improved in all rating scales. There were highly statistical significant differences between panic patients and control group in all components of power spectral analysis in 2nd (VLF, LF and H in supine) and in two component of 3rd (LF and HF in standing) positions. There was also statistically significant difference between these two groups in LF/HF ratio in supine position (2nd). We have found statistically significant differences in HRV frequencies between before and after CBT program in VLF in standing position. We have also found statistically significant differences in HRV frequency ratios in the third position in case of decrease VLF + LF / HF ratio. We can also see decreasing activity in VLF and LF band in standing position in1st measurement and an increase in VLF and LF band in standing position in 2nd measurement.