AIM: To compare heart rate variability (HRV) indices between pulmonary arterial hypertension (PAH) patients and controls, and to investigate whether therapy improves heart rhythm. METHODS: Thirty-eight patients and 20 controls underwent Holter monitoring. HRV was analyzed before and after PAH therapy. Various time, and frequency domain indices of HRV analysis including standard deviation of all normal-to-normal intervals, standard deviation of mean values for all normal-to-normal intervals over 5 min, and square root of the mean square differences of successive RR intervals were recorded and analyzed before and after 1 year of PAH therapy. RESULTS: Significant differences with regard to diminished physical capacity, impared cardiac output, increased BNP in PAH cohort; HRV indices were diminished compared to controls and no differences between before and after PAH therapy with respect to analysis of HRV. Patients exhibited depressed HRV and therapy failed to improve HRV indices suggesting urgent unmet need for better therapeutic options. CONCLUSION: Patients with PAH exhibit severely depressed HRV. Surprisingly, PAH specific therapy for 1 year with phosphodiesterase- 5 inhibitor, prostacyclin analogue, endhotelin receptor antagonist, or their combination failed to improve HRV indices suggesting urgent unmet need for better therapeutic options.