Patellofemoral joint pain and iliotibial band syndrome are very common running-related injuries. Excessive contralateral pelvic drop, hip adduction, and hip internal rotation have been suggested to be associated with the two injuries. The purpose of this repeated measures and the cross-sectional study was to investigate the effect of flat running shoes on these kinematic variables compared with that of conventional running shoes with a 10 mm drop. Eighteen male recreational runners were recruited to run in flat shoes and conventional shoes with a 10 mm drop, in random order. Impact force data and lower extremity kinematics were synchronously obtained using two Kistler force plates and eight motion infrared cameras, whereas differences in the impact force and hip kinematics were compared using statistical parametric mapping. Regarding hip kinematics, the hip flexion (p = 0.004) and adduction angles (p = 0.004) decreased significantly at 30-70% and 62-85% of the stance phase, respectively, while wearing flat running shoes; the contralateral pelvic drop angle (p = 0.001) decreased significantly at 31-75% of the stance phase while wearing flat running shoes. The knee internal rotation angle (p = 0.035) decreased significantly at 8-17% of the stance phase while wearing flat running shoes compared with conventional running shoes. Given that these kinematic variables are associated with patellofemoral joint pain and iliotibial band syndrome, flat running shoes may have potential benefits for the prevention or treatment of knee injuries.