Knowledge of the kinematics and loadings at the lower limb joints at different seat positions during cycling are helpful for the selection of the best seat position for rehabilitation purposes. This study aimed to develop an instrumented cycle ergometer to measure the joint angular and moment changes during cycling at different seat positions. Fifteen healthy young subjects participated in the current study and performed cycling in nine different seat positions. The results showed that seat positions, especially horizontal ones, affected joint loadings. Moving the seat anteriorly loaded the hip flexors and knee extensors while moving the seat posteriorly loaded the hip extensors, knee flexors and ankle plantarflexors. These results will help therapists to decide seat positions most suitable for the rehabilitation of individual patients and for ergonomic bicycle design.