Aim To evaluate the effects of home- and hospital-exercise programs on exercise capacity and chronotropic variables in patients with heart transplantation. Methods Forty patients were randomized into two groups either hospital- or home-based exercise program. The patients were compared, before and after the rehabilitation program, with respect to maximal oxygen uptake (pVO(2)), chronotropic variables [heart rate reserve (HRRe), heart rate recovery (HRR1), and chronotropic response index (CRI)] and Duke Treadmill Score (DTS). Results Hospital-based exercise group has shown a significant recovery in post-exercise pVO(2) (pre-exercise 16.73 +/- 3.9 ml/kg/min, post-exercise 19.53 +/- 3.89 ml/kg/min, P = 0.002) and DTS (pre-exercise 4.74 +/- 1.17, post-exercise 5.61 +/- 1.11, P = 0.002). A significant recovery in favor of the hospital- based exercise group was found in HRRe (pre-exercise 26.9 +/- 14.6, post-exercise 34.6 +/- 14.6, P = 0.01). No significant change was observed in HRR1 (pre-exercise -1.38 +/- 1.04, post-exercise -1.21 +/- 1.89, P = 0.49) and CRI (pre-exercise 0.44 +/- 0.23, post-exercise 0.48 +/- 0.20, P = 0.15) in hospital-based exercise group. No significant change was observed in any parameters of home-based group (P > 0.05). Conclusion A significant recovery was observed both in the functional capacity and the chronotropic response in hospital-based exercise program. Exercise programs that are planned to be performed under supervision in rehabilitation units are useful for the patients with heart transplant in terms of the exercise capacity and chronotropic variables.