This study examined the effects of the lower limb alignment on the pelvis, hip, and knee kinematics in people with genu varum during stair walking. Methods: Forty subjects were enrolled in this study. People who had intercondylar distance ≥ 4cm were classified in the genu varum group, and people who had intercondylar distance < 4cm and intermalleolar distance < 4cm were placed in the control group. 3D motion analysis was used to collect the pelvis, hip, and knee kinematic data while subjects were walking stairs with three steps. Results: During stair ascent, the genu varum group had decreased pelvic lateral tilt and hip adduction at the early stance phase and decreased pelvic lateral tilt at the swing phase compared to the control group. At the same time, they had decreased minimal hip adduction ROM at the early stance and decreased maximum pelvic lateral tilt ROM and minimum hip rotation ROM at the swing phase. During stair descent, the genu varum group had decreased pelvic lateral tilt at the early stance and decreased pelvic lateral tilt and pelvic rotation at the swing phase. In addition, they had decreased pelvic frontal ROM during single limb support and increased knee sagittal ROM during the whole gait cycle. Conclusion: This study suggests that a genu varum deformity could affect the pelvis, hip and knee kinematics. In addition, the biomechanical risk factors that could result in the articular impairments by the excessive loads from lower limb malalignment were identified.