New concept of functional knee phenotypes in Caucasians demonstrated the variability of coronal alignment in knee osteoarthritis (OA), but it remains unclear in Japanese. This study aims to analyze the knee phenotype in advanced varus knee OA for Japanese. In addition, the ethnical difference is discussed. This study analyzed 879 knees involving 186 males (74years) and 693 females (74years). The knee phenotypes were assessed by the definition in Hirschmann's group. The hip-knee-ankle angle (HKA), femoral mechanical angle (FMA) and tibial mechanical angle (TMA) were assessed in CT data according to the coordinate system. The neutral angle was 180° in HKA, 93° in FMA and 87° in TMA. The smaller angle means larger varus angles. The average angle (males, females) of the HKA (170.9 ± 4.3°, 169.4 ± 5.0°), FMA (91.5 ± 2.7°, 90.6 ± 3.0°), and TMA (82.4 ± 3.6°, 82.7 ± 3.7°) demonstrated varus angles with the sex difference (HKA, p < 0.001; FMA, p = 0.001). The phenotypes were 73 types in males and 150 types in females with a mild correlation between the HKA and the FMA or TMA. In 61.3% of males and 52.2% of females, the TMA was greater than the FMA, while the FMA was greater in 16.7% of males and 23.1% of females. There were many functional knee phenotypes with sex differences for advanced varus knee OA in Japanese, showing ethnical differences of larger varus angles compared to those for Caucasians in the previous report. IV.