Effect of boundary layer thickness on the flow characteristics around a rectangular prism has been investigated by using a PIV(Particle Image Velocimetry) technique. Three different boundary layers(thick, medium and thin)were generated in the Atmospheric Boundary Layer Wind Tunnel at Pusan National University. The thick boundary layer having 670 mm thickness was generated by using spires and roughness elements. The medium thickness of boundary layer($\delta$=270 mm) was the natural turbulent boundary layer at the test section floor with fairly long developing length(18 m). The thin boundary layer($\delta$=36.5 mm) was generated on the smooth panel elevated 70cm from the wind tunnel floor. The Reynolds number based on the free stream velocity(3 ㎧) and the height of the model(40 mm) was 7.9$\times$10$^3$. The mean velocity vector fields and turbulent kinetic energy distributions were measured and compared. The effect of boundary layer thickness was clearly observed not only in the length of separation bubble but also in the location of reattachment point. The thinner the boundary layer thickness, the higher the turbulent kinetic energy Peak around the model roofbecame. It is strongly recommended that the height ratio between the model and the approaching boundary layer thickness should be encountered as a major parameter.