Accurate Computational Fluid Dynamics (CFD) simulations of atmospheric boundary layer (ABL) flow are essential for a wide variety of atmospheric studies including pollutant dispersion and deposition. The accuracy of such simulations can be seriously compromised when wall-function roughness modifications based on experimental data for sand-grain roughened pipes and channels are applied at the bottom of the computational domain. This type of roughness modification is currently present in many CFD codes including Fluent 6.2 and Ansys CFX 10.0, previously called CFX-5. The problems typically manifest themselves as unintended streamwise gradients in the vertical mean wind speed and turbulence profiles as they travel through the computational domain. These gradients can be held responsible—at least partly—for the discrepancies that are sometimes found between seemingly identical CFD simulations performed with different CFD codes and between CFD simulations and measurements. This paper discusses the problem by focusing on the simulation of a neutrally stratified, fully developed, horizontally homogeneous ABL over uniformly rough, flat terrain. The problem and its negative consequences are discussed and suggestions to improve the CFD simulations are made.