Cyclists usually change their body position on the saddle depending on the characteristics of the race. We compared the effects of cycling at three body positions on the saddle (preferred/self-selected, most forward, most backward) on pedalling technique for cyclists and triathletes. Twelve cyclists and nine triathletes performed four trials starting with the maximal aerobic workload, followed by three trials at the workload of their ventilatory threshold. Force applied on the right pedal via an instrumented pedal, lower limb kinematics via video and muscle activation via electromyography were recorded during all trials. Pedalling technique was quantified using total force applied on the pedal, pedal force effectiveness, activation of six lower limb muscles, joint angles and mechanical work at the ankle, knee and hip joints. Analyses using effect sizes showed no large effects from changes in position on the saddle for pedal forces, ankle joint work and ankle kinematics. There were large increases in knee joint angle and mechanical work and rectus femoris activation along with smaller hip work at the forward position on the saddle. Differences between cyclists and triathletes were not substantial. Effects of changes in saddle positions were limited to the hip and knee joints.