Vortical structures are identified and studied in databases generated using Large-Eddy-Simulation for turbulent channel flow over several terrain configurations (terrain varying sinusoidally in the streamwise direction, and terrain varying sinusoidally in both the streamwise and spanwise directions). Vortex cores are identified through the method of Jeong & Hussain and are visualized as isosurfaces of negative values of the second largest eigen value of a tensor closely related to the velocity gradient tensor. In both neutral and stably stratified flows over sinusoidally varying terrain, streamwise vortices are a prominent structure of the near wall region. In contrast to channel flows over a flat bed, the location and streamwise extent of these vortices are determined by the wavelength of the sinusoidal terrain. The vortices begin in the reattachment zone of a trough near the upslope surface, continue up over the crest, become detached in a region of shear in the lee, become unstable, and lose their identity in the strong turbulence that characterizes the middle of the trough. Evidence suggests that a Goertler instability mechanism is important in the formation and maintenance of the streamwise vortices