This study presents a three-dimensional numerical analysis of the effect of boundary layer thickness on vortex structures and heat transfer behind a hill mounted in a laminar boundary layer. When the thickness of the velocity boundary layer is comparable to the hill height, a hairpin vortex is formed symmetrically to the center of the spanwise direction in the wake. A secondary vortex is formed between the legs, and horn-shaped secondary vortices appear under the concave parts of the hairpin vortex. When the boundary layer thickness increases, the legs and horn-shaped secondary vortices move toward the center of the spanwise direction, and thus heat transport and heat transfer increase there. At this time, high-turbulence areas generated locally move toward the center of the spanwise direction with an increase in the boundary layer thickness. With a further increase in the boundary layer thickness, steady streamwise vortices are formed downstream of the hill, but the heat transfer decreases. © 2009 Wiley Periodicals, Inc.