A cruise missile is a guided missile that uses a lifting wing and a jet propulsion system to allow sustained flight. Cruise missiles are, in essence, unmanned aircraft and they are generally designed to carry a large conventional or nuclear warhead many hundreds of miles with excellent accuracy. In this study, navigation and control studies on cruise missiles are performed. Due to the variety and complexity of the subsystems of the cruise missiles, the main concern is limited with the navigation system. Navigation system determines the position, velocity, attitude and time solutions of the missile. Therefore, it can be concluded that an accurate self-contained navigation system directly influences the success of the missile. In the study, modern radar data association algorithms are implemented as new Terrain Aided Navigation (TAN) algorithms which can be used with low-cost Inertial Measurement Units (IMU&rsquo / s). In order to perform the study, first a thorough survey of the literature on mid-course navigation of cruise missiles is performed. Then, study on modern radar data association algorithms and their implementations to TAN are done with simple simulations. At the case study part, a six degree of freedom (6 DOF) flight simulation tool is developed which includes the aerodynamic and dynamic model of the cruise missile model including error model of the navigation system. Finally, the performances of the designed navigation systems with the implemented TAN algorithms are examined in detail with the help of the simulations performed.