With expansion of usage of unmanned vehicles, developing accurate and reliable navigation systems is vital . Role of Inertial Navigation System in these navigation systems, due to its independence from external sensors, is undeniable. Inertial Navigation System is consist of an Inertial Measurement Unit which contains three orthogonal accelerometers and three orthogonal gyroscopes. With measurements of these sets and acknowledge of initial position, deadreckoning can be done perfectly. Finding initial misalignment angles between the inertial measurement unit and navigation frame axes is the first and one of the most important steps in the navigation process. Depend on grade of the inertial measurement unit sensors, different types of Initial alignment methods should be used. The majorgoal of this thesiis analysis and correction of the misalignment angles between the inertial measurement unit and navigation frame axes. To deal with this problem, different methods like Optimization based initial alignment, using Kalman filter for estimating alignment errors with measurements of aided sensors like Doppler velocity log and Global positioning system, and a novel method based on global positioning system and Doppler velocity log measurements is provided. At the end, results from these methods are compared for quality assessment of the presented methods. Key Word : Strapdown Inertial Navigation System , Error State Kalman Filter , Optimization , Initial Alignment, Inertial Measurement Unit