In this study, the hierarchical backstepping control (HBC) is used for the trajectory-tracking of autonomous underwater vehicles (AUV) subject to uncertainties (e.g., current disturbances). The proposed HBC utilizes hierarchical structures of the backstepping control based on the kinematic and dynamic models such that both the virtual velocity control and trajectory-tracking of the AUV lead to asymptotic stability. The robustness of the proposed control technique is demonstrated via injection of uncertainties into the closed-loop model. The overall closed-loop stability of the proposed control scheme is guaranteed to have uniformly ultimately bounded (UUB) performance based on the Lyapunov stability criteria. Finally, the feasibility and effectiveness of the proposed scheme are evaluated through computer simulations.