In guided missile systems, reducing terminal-position error is the primary objective of the inertial navigation system. As a seeker is used to sense and track a target, the critical function of the inertial navigation system is to provide the seeker with accurate missile attitude information and help the seeker to keep tracking a target continuously. As inertial sensor body and missile body alignment errors are taken into account, it is desirable to minimize the alignment errors between the missile seeker and the attitude of inertial navigation system. Among the alignment errors, this paper addresses the methods of measuring and compensating misalignment between inertial sensor body and housing frame and shows test results of several experiments.