Roughness effects on a laminar separation bubble, formed on a flat plate boundary layer due to a strong adverse pressure gradient similar to those encountered on the suction side of typical low-pressure turbine blades, are studied by direct numerical simulation. The discrete roughness elements that have a uniform height in the spanwise direction and ones that have a height that is a function of the spanwise coordinate are modeled using the immersed boundary method. The location and the size of the roughness element are varied in order to study the effects on boundary development and turbulent transition; it was found that the size of the separation bubble can be controlled by positioning the roughness element away from the separation bubble. Roughnesses that have a height that varies in a periodic manner in the spanwise direction have a great influence on the separation bubble. The separation point is moved downstream due to the accelerated flow in the openings in the roughness element, which also prevents the formation of the recirculation region after the roughness element. The reattachment point is moved upstream, while the height of the separation bubble is reduced. These numerical experiments indicate that laminar separation and turbulent transition are mainly affected by the type, height, and location of the roughness element. Finally, a comparison between the individual influence of wakes and roughness on the separation is made. It is found that the transition of the separated boundary layer with wakes occurs at almost the same streamwise location as that induced by the three-dimensional roughness element.