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This study accesses the effects of shoe heel heights on loading, muscle activity, and plantar foot pressure of trans-tibial amputees during standing. Five male subjects with unilateral trans-tibial amputation volunteered to participate in this study. Three pairs of shoes with zero, 20 mm, and 40 mm heel heights were used. The loading line of the prosthetic side, the plantar foot pressure, and the surface electromyography (EMG) of 10 muscles were simultaneously recorded. With increasing shoe heel heights during standing, the loading line of the prosthetic side shifted from the anterior to the posterior side of the knee center, the peak pressure was increased in the medial forefoot region, and the peak pressure was reduced in the heel region. The EMG of the medial and lateral gastrocnemius of the sound leg almost doubled and that of the rectus fomris, vastus lateralis, and vastus medialis of the prosthetic side increased to different extents with increasing heel heights from zero to 40 mm. These results show a high correlation with human physical behavior. Changing of the heel heights for trans-tibial amputees during standing actually had similar effects to altering the prosthetic sagittal alignment. The results suggest that an alignment change is necessary to accommodate heel height changes and that prosthesis users should be cautious when choosing shoes.