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In motion analysis marker sets or protocols are mostly developed for gait analysis and it has been shown that the marker set used affects the results of gait analysis. These marker sets are also used for the analysis of high dynamic sports movements. Single-leg landings are a common tool to investigate functional knee stability and further to predict injury risks where frontal plane motion and loading seem to play an important role. Until now, it is unknown how the marker sets affect the motion analysis results of such high dynamic movements. Therefore, the aim of the study was to compare six different marker sets. Three-dimensional motion and force data of single-leg landings in 12 healthy subjects were collected. Six different marker sets consisting of up to 26 markers and two clusters were simultaneously attached to the subjects’ lower limb and pelvis. The results show that particularly, the knee joint angles in the frontal and transverse plane showed the greatest differences between marker sets with in part contrary joint angle directions and great differences in angle magnitude. In addition, the amount of joint load was dependent on the marker set used for analysis. These results show that one must be careful when interpreting and comparing data of the frontal or transverse plane during high dynamic movements.