In the case of a strapdown inertial navigation system (SDINS) with sizeable attitude errors, the uncertainty caused by linearization of the system degrades the performance of the filter. In this paper, a robust filter and various error models for the uncertainty are presented. The analytical characteristics of the proposed filter are also investigated. The results show that the filter does not require the statistical property of the system disturbance and that the region of the estimation error depends on a freedom parameter in the worst case. Then, the uncertainty of the SDINS is derived. Depending on the choice of the reference frame and the attitude error state, several error models are presented. Finally, various in-flight alignment methods are proposed by combining the robust filter with the error models. Simulation results demonstrate that the proposed filter effectively improves the performance.