Purpose To evaluate the effects of a structured hand cycle training programme on physical capacity in subjects with spinal cord injury (SCI) during clinical rehabilitation. Method Twenty subjects with SCI who followed hand cycle training were compared with matched control subjects from a Dutch longitudinal cohort study, who received usual care. Primary outcomes of physical capacity were peak power output (POpeak), peak oxygen uptake (VO2peak) and oxygen pulse during a hand rim wheelchair test. Secondary outcome measures were isometric peak muscle strength of the upper extremities and pulmonary function. Hand cycle capacity (POpeak and VO2peak) was evaluated in the training group only. Results Strong tendencies for improvement were found in wheelchair capacity, reflected by POpeak and oxygen pulse after additional hand cycle training. Significant effects on shoulder exo- and endo-rotation and unilateral elbow flexion strength were found but no improvements on pulmonary function. Conclusions Additional hand cycle training during clinical rehabilitation seems to show similar or slightly favourable results on wheelchair capacity and muscle strength compared with regular care. The heterogeneous subject group and large variation in training period may explain the limited effects of additional hand cycle training on wheelchair capacity. © 2010 Informa UK, Ltd.