Laboratory-based gait analyses traditionally analyze baseline characteristics in individuals while they are barefoot. However, there is limited evidence on whether individuals’ preferred walking shoes alter lower extremity kinematics during over-ground walking. We present novel evidence regarding the effects of shoes on lower extremity kinematics in healthy, young adults. Fifteen volunteers participated in this study which obtained lower extremity kinematic data on two over-ground walking conditions (barefoot and preferred shoes). Gait velocity, stance width, and stride length, along with sagittal plane hip, knee, and ankle angular positions were computed;​ hip, knee, and ankle positions were normalized to 100% of the stride. Dependent t-tests were used to compare baseline and shoe conditions for gait velocity and stance width;​ a two-way analysis of variance was used for stride length. A point-by-point Model Statistic analysis was used to identify significant differences in angular joint positions between conditions. Our results indicate that shoes affected the ankle angular joint position for more than half of the gait cycle, and affected the knee angular joint position, but only for approximately 20% of the cycle. The hip was unaffected by shoes. Gait velocity and stance width were statistically significant, with gait velocity being greater for shoes, and stance width being greater while barefoot. Stride length was not statistically significant between conditions. These outcomes suggest that researchers should use caution if they are considering a barefoot condition as a ‘baseline’ for healthy, young adults, as there are marked changes in the ankle, and in traditional gait metrics.