Abstract: Objective To determine the acute effects of heel-to-toe drops (5mm, 0mm, -11mm) of running shoes on the loading of the patellofemoral joint and Achilles tendon (AT) in runners with patellofemoral pain (PFP) during running. Methods Sixteen runners with PFP ran in running shoes in different heel-to-toe drops while retroreflective markers and ground reaction force were required by applying infrared motion capture system and a three-dimensional force plate. Patellofemoral joint stress (PFJS), AT force were calculated based on biomechanical models of patellofemoral joint and AT. Results When PFP runners ran in negative heel shoes, the PFJS during 39%-47% of the stance phase(P<0.001), the maximum PFJS during the stance phase and cumulative PFJS(P<0.05) was lower than positive heel shoes, while the AT force during 12%-46% of the stance phase(P<0.001) and cumulative AT force(P=0.001) was greater than positive heel shoes. Additionally, the AT force during 12%-31% of the stance phase(P<0.001) and cumulative AT force in negative heel shoes was greater in zero heel shoes. Conclusions Running in negative heel shoes decreases the PFJS and cumulative PFJS compared with positive heel shoes, potentially reducing the risk of further development of PFP. However, it increases AT force and the cumulative AT force compared with zero and positive heel shoes, which may increase the risk of AT injury.