In this paper, a two-stage initial alignment scheme is proposed to enhance the operational performance of underwater vehicles with a strapdown inertial navigation system (SDINS) that are widely used for attitude control of underwater and/or aerial movement. For underwater vehicles dropped from and operated with an off-line connection to a mother ship, the application of conventional initial alignment methods is insufficient to achieve a satisfactory attitude control partly due to oscillations in the loading section and/or operating conditions in the mother ship. The proposed technique based on a coarse alignment algorithm is composed of two stages: In the first stage, an alignment on board a ship is performed to set initial values of an underwater vehicle for navigation and control. The second stage, which is performed under the sea, includes a process to correct the initial alignment errors resulting from the first stage alignment. The evaluation study has been conducted for the proposed approach through computer simulation, hardware-in-the-loop simulation (HILS), and sea trials. Evaluation results are presented and discussed.