In paraplegic patients, shoulder complaints attributable to muscle dysbalances arising from the particular daily form of exercise are often observed. The goal of therapy is to correct these imbalances through muscular training, whereby eccentric exercise might offer advantages due to lower fatigue with concurrent higher maximum strength. This study therefore examines muscle fatigue, maximum strength, and suitability for paraplegics of eccentric exercise of the shoulder. Muscle fatigue, isokinetic peak torque, and EMG activity were determined eccentric (Ecc) and concentric (Con) in 41 paraplegic subjects (13 early rehabilitants; 16 trained in wheelchair sports; 12 untrained). Serum CK, myoglobin, and subjective pain were collected for one week after exercise. In eccentric exercise, there was less muscle fatigue in all groups. Highest Ecc/Con peak torque ratio was found in trained subjects in all movements, followed by the untrained and the early rehabilitants. EMG-activity was lower in eccentric compared to concentric exercise (Ecc/Con ratio <1). CK and myoglobin concentrations, like pain symptoms, showed a marked increase after exercise. It is concluded that the Ecc/Con strength patterns among paraplegics are altered. Eccentric exercise offers advantages on the basis of lower muscular fatigue independent of training status and lesion time and higher maximum strength with increasing duration of paraplegia and additional athletic training. However, due to structural damage and subjective pain eccentric exercise can only be recommended with reservations in therapy and training.