Robust adaptive nonlinear control of permanent magnet stepper motors is considered in this paper. The control design methodology is based on our earlier work. A controller is designed for a detailed model of the motor that accounts for the cogging torque and nonsinusoidal flux distribution in the airgap and is robust to parametric and dynamic uncertainties in the entire electromechanical system and achieves reduced torque ripple. The uncertainties are shown to be bounded by polynomials in the states. An adaptive torque profile is designed for the motor that possesses desirable robustness properties. Thereafter, a sinusoidal commutation scheme is utilised to formulate desired phase currents that would generate the desired torque. Voltage level control inputs are designed using backstepping and the robust control design methodology to track the desired currents. The overall stability of the system is shown using Lyapunov techniques. The tracking errors are shown to be globally uniformly bounded. Simulation results are provided to illustrate the efficacy of the advocated approach.