The present work presents the development of a Large Eddy Simulation (LES) methodology viable for complex geometries and suitable for the simulation of rod-bundles. The use of LES and Direct Numerical Simulation (DNS) allows for a deeper analysis of the flow field and the use of stochastical tools in order to obtain additional insight into rod-bundle hydrodynamics. Moreover, traditional steady-state CFD simulations fail to accurately predict distributions of velocity and temperature in rod-bundles when the pitch (P) to diameter (D) ratio P/D is smaller than 1.1 for triangular lattices of cylindrical pins. This deficiency is considered to be due to the failure to predict large-scale coherent structures in the region of the gap. The main features of the code include multi-block capability and the use of the fractional step algorithm. As a Sub-Grid-Scale (SGS) model, a Dynamic Smagorinsky model has been used. The code has been tested on plane channel flow and the flow in annular ducts. The results are in excellent agreement with experiments and previous calculations.