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The lower limbs of children aged 3–9 years present varying knock-knee deformities that have a direct impact on the diversification of the load-bearing axis of the valgus limb and on the modification of gait kinematics. The purpose of our study was to establish the reference values of knee alignment in a Greek population and whether this is linked to a change in the physical activity of children depending on the severity of the genu valgum. Using a clinical method, we measured both the tibiofemoral (TF) angle and the intermalleolar (IM) distance of the lower extremities of normal children. Subsequently, forms of the Netherlands Physical Activity Questionnaire (NPAQ) for young children and the Baecke questionnaire on habitual physical activity, modified especially for children, were completed by the parents. We examined both the development of the TF angle and the IM distance in relation to age and the degree of restriction of physical activity in relation to the severity of the genu valgum. We analysed 316 unaffected lower extremities in children aged 3–9 years. The average value of the TF angle starts around 7° at the age of 3 years and gradually decreases to 4° at the age of 7–8 years. The average value of the IM distance ranges over 3.5 cm at the age of 3 years and progressively decreases to 2 cm at the age of 7–8 years. Physical activity appears to be influenced by sex and the severity of the genu valgum. We provide age-specific values for limb alignment and joint orientation of the lower extremity in children aged 3–9 years. A statistical correlation between all indexes (sport, leisure time and total) of the Baecke and the NPAQs and measurements of genu valgum was noted depending on the severity of the valgus deformity. The level of evidence is the level II Prognostic Study.