Exercise training is a useful component of weight maintenance programmes. Although energy expenditure, not intensity or duration, seems to determine the amount of weight loss attributable to exercise, it is not clear whether changes in the components of body mass are also insensitive to these parameters. Thus, the aim of the present study was to compare the effect of two isoenergetic exercise training programmes, one of low and one of high intensity, on body composition. Fourteen healthy premenopausal untrained women were divided into two equivalent groups, which exercised on treadmill at 45 or 72 % of V(O2max) four times a week for three months, spending 1548 kJ (370 kcal) per exercise session. No dietary intervention was applied. Body mass decreased significantly in both groups but more in the low-intensity than the high-intensity group (by mean +/- SD, 3.3 +/- 1.3 vs. 1.9 +/- 0.9 kg, p = 0.032). The decrease in fat mass was significant in both groups (3.1 +/- 1.2 vs. 2.4 +/- 1.5 kg, respectively) but not significantly different between them. Fat-free mass did not change significantly in either group, although the difference between groups tended to be significant (decrease by 0.2 +/- 0.7 kg in the low-intensity group vs. increase by 0.5 +/- 0.6 kg in the high-intensity group, p = 0.058). In conclusion, exercise training at 45 % of V(O2max) without dietary restriction produced a higher weight loss than at 72 % of V(O2max), whereas the higher intensity tended to maintain fat-free mass, possibly, in part, through the smaller weight loss. Thus, both programmes may prove useful in eliciting favourable changes depending on which target (weight loss or maintenance of fat-free mass) is of higher priority.