The effect of exercise training on heart rate variability (HRV) and improvements in peak oxygen consumption (VO2peak) was examined in sedentary middle-aged men. The HRV and absolute and relative VO2peak of training (n = 19) and control (n = 15) subjects were assessed before and after a 24-session moderate intensity exercise training programme. Results indicated that with exercise training there was a significantly increased absolute and relative VO2peak (P < 0.005) for the training group (12% and 11% respectively) with no increase for the control group. The training group also displayed a significant reduction in resting heart rate; however, HRV remained unchanged. The trained subjects were further categorized into high (n = 5) and low (n = 5) HRV groups and changes in VO2peak were compared. Improvements in both absolute and relative VO2peak were significantly greater (P > 0.005) in the high HRV group (17% and 20% respectively) compared to the low HRV group (6% and 1% respectively). The groups did not differ in mean age, pretraining oxygen consumption, or resting heart rate. These results would seem to suggest that a short aerobic training programme does not alter HRV in middle-aged men. Individual differences in HRV, however, may be associated with VO2peak response to aerobic training.