Background Achieving proper rotational alignment of the femoral component in total knee arthroplasty (TKA) for valgus knee is challenging because of lateral condylar hypoplasia and lateral cartilage erosion. Gap-based navigation-assisted TKA enables surgeons to determine the angle of femoral component rotation (FCR) based on the posterior condylar axis. This study evaluated the possible factors that affect the rotational alignment of the femoral component based on the posterior condylar axis. Materials and methods Between 2008 and 2016, 28 knees were enrolled. The dependent variable for this study was FCR based on the posterior condylar axis, which was obtained from the navigation system archives. Multiple regression analysis was conducted to identify factors that might predict FCR, including body mass index (BMI), Kellgren-Lawrence grade (K-L grade), lateral distal femoral angles obtained from the navigation system and radiographs (NaviLDFA, XrayLDFA), hip-knee-ankle (HKA) axis, lateral gap under varus stress (LGVS), medial gap under valgus stress (MGVS), and side-to-side difference (STSD, MGVS - LGVS). Results The mean FCR was 6.1 degrees +/- 2.0 degrees. Of all the potentially predictive factors evaluated in this study, only NaviLDFA (beta = -0.668) and XrayLDFA (beta = -0.714) predicted significantly FCR. Conclusions The LDFAs, as determined using radiographs and the navigation system, were both predictive of the rotational alignment of the femoral component based on the posterior condylar axis in gap-based TKA for valgus knee. A 1 degrees increment with NaviLDFA led to a 0.668 degrees decrement in FCR, and a 1 degrees increment with XrayLDFA led to a 0.714 degrees decrement. This suggests that symmetrical lateral condylar hypoplasia of the posterior and distal side occurs in lateral compartment end-stage osteoarthritis with valgus deformity.