BACKGROUND The quantification of heart rate variability (HRV) is a tool to assess the interaction between exercise and autonomic control, as well as the pathophysiology of diseases affecting autonomic function. Little is known about the influence of genetically influenced physiology on exercise-induced changes in autonomic cardiac regulation. It was theorised that preintervention values for blood pressure, VO2max, body mass index (BMI), autonomic function and gender contribute significantly to the exercise-induced changes in HRV. METHODS A 12-week, medium-to-high intensity exercise intervention was completed by 183 volunteers (18-22 years). Data were sampled at baseline and after 12 weeks. Standard time domain, frequency domain and Poincaré HRV quantification techniques were implemented. Regression analysis was performed to determine the influences of the predictors (baseline values for low frequency  (LF), high frequency (HF), BMI, VO2max, gender, blood pressure) on the exercise-induced response of the dependent variables (changes in HRV-indicator values). RESULTS Parameters found to be significant (p<0.05) predictors of exercise-induced changes were LF, HF and systolic blood pressure in, respectively, 10, 5 and 2 of the 12 regressions performed. The results indicated that the independent variables contribute between 12.83% and 29.82%, depending on the specific HRV indicator, to the exercise-induced changes in the autonomic nervous system. CONCLUSIONS Preintervention autonomic status, as represented specifically by LF, is the most important determinant of cardiac autonomic response to an exercise intervention in a healthy study population. Baseline autonomic function could thus be a significant confounder in the outcome of exercise study results.