Motion capture systems are used in the analysis and interpretation of athlete movement patterns for a variety of reasons, but data integrity remains critical regardless. The extent to which marker location or constraining degrees of freedom (DOF) in the biomechanical model impacts on this integrity lacks consensus. Ten elite academy footballers performed bilateral overhead squats using a marker-based motion capture system. Kinematic data were calculated using four different marker sets with 3DOF and 6DOF configurations for the three joint rotations of the right knee. Root mean squared error differences between marker sets ranged in the sagittal plane between 1.02 and 4.19 degrees to larger values in the frontal (1.30-6.39 degrees) and transverse planes (1.33 and 7.97 degrees). The cross-correlation function of the knee kinematic time series for all eight marker-sets ranged from excellent for sagittal plane motion (>0.99) but reduced for both coronal and transverse planes (<0.9). Two-way ANOVA repeated measures calculated at peak knee flexion revealed significant differences between marker sets for frontal and transverse planes (p < 0.05). Pairwise comparisons showed significant differences between some marker sets. Marker location and constraining DOF while measuring relatively large ranges of motion in this population are important considerations for data integrity.