The γ-Reθt transition model was adopted to predict the boundary layer transition on Japan Aerospace Exploration Agency (JAXA) high-lift configuration model. A comparison among fully turbulent computation, computation with transition model and wind tunnel test was conducted. Lift and drag characteristics were discussed based on pressure coefficient distributions at several wing sections. Boundary layer transition position was compared with wind tunnel experiment result by checking starting position of intermittency of the γ-Reθt, transition model and distribution of skin friction coefficient. Predicted transition position agreed with experimental results except for the inboard section of mother wing and engine nacelle. To investigate the cause of discrepancy between the computation and experiment, crossflow velocity component within the boundary layer was visualized and it was shown that the large crossflow velocity was seen at inboard section of mother wing where the discrepancy appears significantly. Surface flow visualization using oil flow was carried out to see the flow characteristics on the slat.