Linear bearings are widely used to sustain positioning systems for machine tools. A linear bearing consists of a linear guide rail, rolling elements, and a carriage. For most positioning systems employing linear bearing, the guide rail error is closely related to the precision of the systems. In this study, the motion accuracy of linear roller bearings (LRBs) on the guide rail with vertical waviness error were investigated. To obtain the displacement of the carriage on the erroneous guide rail, a simulation model considering the contact surface deformation between the roller and carriage and between the roller and rail was developed. A flexible body model considering the carriage deformation due to contact load was also considered. The guide rail error was assumed to be harmonic with the period of consecutive clamping bolts because of bolt fastening to clamp the guide rail on the base. The contact loads of the LRBs were calculated with varying the amount of guide rail waviness error using the rigid body model, and the displacements due to the guide rail error was calculated. Then, to obtain the total displacement of the carriage, the elastic deformation of the carriage was calculated using the contact loads obtained from the rigid body model. The motion errors when the carriage moves along the guide rail with waviness error were calculated with varying the amount and period of waviness error. A rigorous investigation was made on the correlation between the carriage length and the interval of fastening bolts.