Measurement of three-dimensional lower limb joint angles are useful to evaluate changes of movements after various lower limb diseases or injuries. However, estimation of three-dimensional angles with inertial measurement units (IMUs) causes errors, especially in abduction/adduction angle and in internal/external rotation angle. This was considered to be caused by difference between the sensor coordinate system and the body coordinate system. In order to solve the problem, various calibration methods of the coordinate system have been proposed. In this paper, three calibration methods, which were selected based on practical application, were examined in estimation of three-dimensional angles of a rigid body model under the 8 attachment conditions of IMU. The Method A determined the body coordinate system by measuring the vertical axis during a standing upright posture and another posture in the sagittal plane. The Method B estimated the sagittal plane and the normal vector of the plane from measured acceleration signals during movement of each segment of the lower limb in the sagittal plane. Method C was similar to Method A, in which postures of vertical and horizontal positions of lower limbs were used. Difference of the coordinate system of the IMU increased significantly RMSE values of estimated angles. Since the Method A and C showed almost same RMSE values as in the case that there was no difference of the coordinate system, the methods are considered to be practical. However, the Method B that used movement in the sagittal plane could not decrease RMSE values in many attachment conditions. Performing the movement in the sagittal plane was considered to be difficult for practical use.