Competitive cyclists have a high incidence of patellofemoral (PF) pain. Deviation of the knee from an optimal pedaling pattern is a contributor to PF pain, but such deviation can be altered by correctly fitting the cyclist to the bicycle. Wedges are used at the shoe-pedal interface (SPI) to alter specific cycling kinematics, but the efficacy of such intervention has not been established. Moreover, determination of efficacy often requires high-cost 3D motion analysis equipment. This study examined cycling kinematics in response to SPI wedges and the morphological differences between cyclists with and without patella-femoral pain. The reliability and precision of Retul, a lower-cost cycling-specific motion capture system, was compared to that of the the “gold standard” Vicon 3D system. Nineteen competitive female cyclists pedaled on a computer-controlled cycle ergometer at 85rpm and 70% of their peak power output. Wedges were 2 and 4 in size, inclined laterally and then medially and were bolted to the SPI. Kinematics were captured using a 10-camera Vicon MX system and then compared with the Retul system. Electromyographic (EMG) output was captured using a wireless 16-electrode surface EMG system. Knee morphology was measured using standing tibiofemoral angle (sTFA) from Vicon data, and foot morphology using the foot posture index (FPI-6) and foot mobility magnitude (FMM) scores. Influence of wedge condition, PF pain history, and morphology on cycling kinematics and EMG were examined with multivariate tests. Regression tests examined the predictive capability of frontal plane knee measurements and knee/foot morphology to determine presence of PF pain.Comparison of Vicon and Retul systems indicated acceptable agreement for hip, knee and ankle joint angle, range of motion and knee distance measurements. Wedges at the SPI altered cycling kinematics, reduced hip flexion, hip extension, and ankle ROM, increased knee range of motion (ROM), and reduced knee distance from bicycle centerline, but did not alter vastus medialis (VM) or vastus lateralis (VL) EMG. The presence of pain was predicted by knee distance to bicycle centerline, knee frontal angle while cycling and FMM score. There were significant differences between those with and without PF pain for the temporal aspects of EMG and foot/lower limb morphology. Cycling with the knee farther from the bicycle and with a more valgus knee angle predicted PF pain group classification. Overall, wedges at the SPI alter knee kinematics and the temporal characteristics of VM and VL muscles of competitive female cyclists. Cyclists with PF pain demonstrate different morphologic, kinematic and EMG patterns than those with no pain. These data support the use of the wedges at the SPI for altering cycling kinematics and support the use of Retul as a low-cost 3D motion analysis system for measuring cycling kinematics.