In this study, the boundary element method is formulated to evaluate hydrodynamic characteristics of bodies including free surface effect. The method is based on two equations, the perturbation potential boundary integral and the pressure Kutta condition, which are solved simultaneously. The method uses isoparametric elements for both quantity and geometric on the boundary. The method is first applied to two three-dimensional bodies (hydrofoil and vertical strut) of the NACA4412 profiles and symmetric Joukowski with 12% thickness. It is assumed that hydrofoil moves in constant speed. Some results of the pressure distribution, lift, wave-making drag and wave pattern are presented. It is shown that the computational results are in good agreement with the experimental measurements and other calculated values.