Background <p>Data about efficacy of different training modalities during rehabilitation of horses with back pain is scarce. The aim of this study was to analyze the effect of water treadmill training, lunging and dry treadmill training in horses with back pain.</p> Materials and methods <p>Eighteen warmblood riding horses referred with confirmed clinical signs of back pain including abnormal responses to passive mobilisation were randomized into three groups to participate in a 6-week water treadmill training, lunging or dry treadmill program under otherwise identical conditions. Two clinicians, one blinded to the program, performed a structured clinical examination of the back at three time-points (baseline, week 3, week 6). Mechanical nociceptive thresholds were determined with pressure algometry.</p> Results <p>Visual muscle development scores for the lumbar region (<i>p</i> = 0.001) and palpation sensitivity scores along the thoracic and lumbar region significantly improved at week 6, compared to baseline (<i>p</i> &lt; 0.001). No differences in mechanical nociceptive thresholds were detected between water treadmill training, lunging and dry treadmill training at any time-point (<i>p</i> &gt; 0.05). At week 3 and 6 of all programs mechanical nociceptive thresholds significantly increased at the level of the 10th to 18th thoracic (T18) and 3rd lumbar vertebra (L3) compared to baseline.</p> Discussion/Main limitations <p>Small group size, lack of control group with ridden rehabilitation exercise.</p> Conclusions <p>Different training programs without a rider could be beneficial for horses with back pain. Water treadmill training seems equivalent to dry treadmill training and lunging to increase mechanical nociceptive thresholds in the region with main saddle contact.</p>