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A vital necessity for any kind of inertial navigation system (INS) is the alignment of its axis with the vehicle body frame (VBF). Civilian vehicle navigation has strict requirements with respect to cost, size, reliability, and ease of implementation of the system. Microelectromechanical system (MEMS) inertial sensors have satisfied the cost and size requirements for civilian vehicle navigation; however, reliability and ease of implementation of these low-cost and miniaturized navigation systems are still parts of major research and investigation. This paper focuses on an important aspect of the ease of implementation for inertial sensors. From a civilian user perspective, accurately aligning the inertial system with respect to the vehicle, before every use, is not a desirable quality for a portable navigation system. In addition, it is not realistic to assume that even a careful user can achieve good alignment accuracy of the system. The purpose of this paper is to investigate the effects of misalignment errors that will produce errors in initial alignment and affect the navigation accuracy for two different inertial systems. The inertial systems are classified according to the number of sensors used in the system. The first system consists of three gyros and three accelerometers [full inertial measurement unit (IMU)], whereas the second system only has one gyro and two horizontal accelerometers (partial IMU).