AIM: The study assessed the effects of different weekly training frequencies performed over a 12 week exercise programme (strength, endurance, balance) on autonomic cardiac activity, blood pressure and cardiorespiratory fitness (CRF) in elderly individuals. METHODS: Fifty-eight individuals participated in the study: 2TG (N=24, 71.1+/-6.4 yrs; 19 females, 5 males) performing two, 60min sessions/week; and 3TG (N=34, 72.3+/-7.9 yrs; 25 females, 9 males) performing three, 60min sessions/week. Time domain and spectral analysis of heart rate variability (HRV) quantified autonomic cardiac regulation. RESULTS: Natural logarithm (Ln) transformation was applied to all HRV parameters. There were significant reductions in total power (Ln TP) (p=0.006), low frequency (Ln LF) (p=0.013), high frequency (Ln HF) (p=0.013) and root mean square of successive differences (Ln rMSSD) (p=0.014) post training in 3TG after intervention. Diastolic BP (DBP) decreased significantly in both groups (2TG: P<0.001; 3TG: P<0.001). Both groups showed significant improvements in six-minute walk distance (2TG: P=0.003, 3TG: P=0.001). However, there were significant HRV differences between 2TG and 3TG for Ln TP (P=0.018), Ln LF (P=0.049), Ln HF (P=0.039) and Ln rMSSD (P=0.049). CONCLUSIONS: A combined exercise programme resulted in improved DBP and CRF irrespective of training two or three 60min sessions/week. However, training three, sessions/week induced negative health-related changes in autonomic cardiac activity through reducing HRV parasympathetic function, while HRV was maintained in the group training twice a week.