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The habitual motion path theory predicts that humans tend to maintain their habitual motion path (HMP) during locomotion. The HMP is the path of least resistance of the joints defined by an individual’s musculoskeletal anatomy and passive tissue properties. Here we tested whether participants with higher HMP deviation and whether using footwear that increases HMP deviation during running show higher reductions of knee joint articular cartilage volume after 75 minutes of running. We quantified knee joint articular cartilage volumes before and after the run using a 3.0-Tesla MRI. We performed a 3D movement analysis of runners in order to quantify their HMP from a two-legged squat motion and the deviation from the HMP when running in different footwear conditions. We found significantly more cartilage volume reductions in the medial knee compartment and patella for participants with higher HMP deviation. We also found higher cartilage volume reductions on the medial tibia when runners wore a shoe that maximized their HMP deviation compared with the shoe that minmized their HMP deviation. Runners might benefit from reducing their HMP deviation and from selecting footwear by quantifying HMP deviation in order to minimize joint cartilage loading in sub-areas of the knee.