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Habitually barefoot (HB) children from the Kalenjin tribe of Kenya are known for their high physical activity levels. To date, there has been no comprehensive assessment of foot structure and function in these highly active and HB children/adolescents and link with overuse injuries. Purpose: The aim of this research is to assess foot structure, foot function, injury and physical activity levels in Kenyan children and adolescents who are HB compared with those who were habitually shod (HS). Methods: Foot structure, function, injury prevalence, and physical activity levels were studied using two studies with equal numbers of HS and HB. HS and HB children and adolescents were matched for age, sex, and body mass. Foot arch characteristics, foot strength, and lower-limb injury prevalence were investigated in Study 1 (n = 76). Heel bone stiffness, Achilles tendon moment arm length and physical activity levels in Study 2 (n=62). Foot muscle strength was measured using a strength device TKK 3360 and heel bone stiffness by bone ultrasonometry. The moment arm length of the Achilles tendon was estimated from photographs and physical activity was assessed using questionnaires and accelerometers. Results: Foot shortening strength was greater in HB (4.8 ± 1.9 kg vs 3.5 ± 1.8 kg, P < 0.01). Navicular drop was greater in HB (0.53 ± 0.32 cm vs 0.39 ± 0.19 cm, P < 0.05). Calcaneus stiffness index was greater (right 113.5 ± 17.1 vs 100.5 ± 116.8, P < 0.01 left 109.8 ± 15.7 vs 101.7 ± 18.7, P < 0.05) and Achilles tendon moment arm shorter in HB (right, 3.4 ± 0.4 vs 3.6 ± 0.4 cm, P < 0.05; left, 3.4 ± 0.5 vs 3.7 ± 0.4 cm, P < 0.01). Lower-limb injury prevalence was 8% in HB and 61% in HS. HB subjects spent more time engaged in moderate to vigorous physical activity (60 ± 26 min·d−1 vs 31 ± 13 min·d−1; P < 0.001). Conclusions: Significant differences observed in foot parameters, injury prevalence and general foot health between HB and HS suggest that footwear conditions may impact on foot structure and function and general foot health. HB children and adolescents spent more time engaged in moderate to vigorous physical activity and less time sedentary than HS children and adolescents.