BACKGROUND: Atrial fibrillation (AF) and hypertension are independently associated with impaired autonomic function determined using heart rate variability (HRV). As these conditions frequently co-exist, we sought to determine whether AF would worsen HRV in hypertensive patients. DESIGN: We studied HRV in AF (and hypertension) (n = 61) and hypertension control group (n = 33). The AF (and hypertension) group was subdivided into permanent AF (n = 30) and paroxysmal AF (n = 31) and re-studied. Time-domain, frequency-domain and nonlinear measures of HRV were determined. Permanent AF group (n = 30) was followed up after 8 weeks following optimisation of their heart rate and blood pressure (BP). RESULTS: Time-domain and nonlinear indices of HRV were higher in AF (and hypertension) group compared to hypertensive controls (P </= .01). Time-domain and nonlinear indices of HRV were higher in permanent AF group compared to paroxysmal AF (P </= .001). Permanent AF was an independent predictor of HRV on multivariable analysis (P = .006). Optimisation of heart rate and BP had no significant impact on HRV in permanent AF. CONCLUSIONS: AF, independent of hypertension, is characterised with marked HRV and is possibly related to vagal tone. HRV is higher in permanent AF compared to paroxysmal AF suggesting evident autonomic influence in the pathophysiology of permanent AF. Modulation of autonomic influence on cardiovascular system should be explored in future studies.