Secondary flow characteristics like horseshoe vortices and related total pressure losses decrease turbine efficiency. Computerized simulations of potentially favorable modifications in turbine systems could provide a fast, numerical and inexpensive method of evaluating their effects on flow properties: This paper consists of a comparative numerical study of the flow characteristics of a domain containing a vertical cylinder subjected to cross flow and upstream endwall modifications. Analyzing the flow around a turbine nozzle guide vane (NGV) could be simplified by modeling it as a vertical cylinder with a diameter proportional to the leading edge diameter of the blade, and adding upstream endwall fences of varying dimensions and alignments could attenuate the development of a horseshoe vortex. A commercial computational fluid dynamics (CFD) software package, Fluent, was used for the numerical analysis. To validate the modeling strategy, experimental data previously reported in the literature for conventional cylinders in cross flow were compared to the current predictions. A grid independence study was also performed. The lateral distance between the two legs of the horseshoe vortex downstream of the cylinder was decreased by 7% to 14%. All fence types effectively changed the location of the main horseshoe vortex roll-up. The height of the fence was more influential than the length of the fence in modifying flow characteristics. The existence of the fences slightly increased the mass-averaged total pressure loss far downstream of the cylinder; however, beneficial near-fence flow characteristics were observed in all cases. Also, it was noted that an endwall fence could possibly result in decreased interaction between the horseshoe vortices created by consecutive blades in a row of NGV blades, which would be expected to result in improved flow conditions within actual turbine passages.