OBJECTIVES: Patients with chronic kidney disease (CKD) are at a high risk of future autonomic dysfunction and cardiovascular disease. The aim of this study was to examine the effects of a 12-month lifestyle intervention (LI) involving regular aerobic exercise on cardiac autonomic function in CKD patients. DESIGN: Pooled exploratory analysis. METHODS: 113 eligible patients with stage 3-4 CKD (eGFR 25-60 ml/min/1.75m(2)) participated in a LI program, including an 8-week individualised gym-based exercise program followed by a 10-month home-based program. The control (CON) group underwent standard nephrological care. The following parameters were assessed prior to and following the 12-month study period: cardiorespiratory fitness (VO(2)peak) from a graded exercise test; cardiac autonomic function from time, frequency, and non-linear measures of heart rate variability (HRV), heart rate (HR) recovery following peak exercise, and chronotropic competence during exercise. RESULTS: Compared to the CON group, the LI group significantly increased VO(2)peak (CON = -1.0 vs. LI = +1.8 ml/kg/min, p < 0.01) while there was no significant improvement in any HRV measure (p = 0.85), HR recovery (p = 0.38) or chronotropic competence (p = 0.28). Changes in relative VO(2)peak were significantly associated with changes in a non-linear HRV measure, alpha1 (p < 0.01), independent of age and eGFR (r(2) = 0.196, p = 0.03). CONCLUSIONS: Despite the significant increase in cardiorespiratory fitness for the LI group, there were no changes in cardiac autonomic function. However, alpha1 may be a sensitive measure to assess VO(2)peak changes in this clinical cohort. Further research is required to investigate the role of different modalities of exercise training to enhance cardiac autonomic function in patients with CKD.