Knowledge of femoral and tibial morphology is important for patient-specific surgery in both joint reconstruction and preservation procedures. Studies evaluating morphological variance in femoral and tibial alignments in Asian populations are scarce. This is the first descriptive study evaluating the femoral and tibial phenotypes of varus alignment in a Southeast Asian population. Long-leg coronal standing radiographs of 2021 limbs were obtained, and the hip-knee-ankle angle, mechanical lateral distal femoral angle, medial proximal tibial angle and joint line convergence angle were measured. Joint line obliquity was calculated, and the knees were classified according to the Coronal Plane Alignment of Knee (CPAK) classification. Descriptive analyses on alignment parameters and demographic data (age, gender, ethnicity and body mass index [BMI]) were performed and entered into a linear regression model. The highest frequency of limb alignment in the population was found to be CPAK type I (52.71%, n = 1003). Tibial varus was the largest contributor of varus malignment. Of the varus knees (n = 1247), varus deformity was found solely in the tibia (68.60%), solely in the femur (2.07%) and was contributed by both the femur and the tibia (4.97%). In the linear regression model, BMI was found to be a strong determinant for femoral varus (P = 0.004) and joint line incongruence (P < 0.001). The findings of this study will be important to surgeons during planning for joint preservation procedures (such as corrective osteotomies) and joint arthroplasties to restore alignment.