Ventilation systems are used for create a thermally comfortable environment and good indoor air quality. It is therefore essential to have adequate tools for predicting the performance of these systems. Among the various approachs, the computational fluid dynamics could be a useful tool for the design of the ventilation system. When dealing with pollutants dispersion problems, a steady state averaged simulation can be misleading because it is not able to properly predict and model peak concentrations, which can be relevant even if temporary. An interesting approach is the use of LES (Large Eddy Simulations) simulations to obtain a better description of concentrations oscillations. In this framework, the aim of this work is the validation of simulation carried out using the FDS (Fire Dynamic Simulator) software with an actual case study, already studied with a mock-up. Secondly, two new configurations of the ventilation system are proposed, in order to stress the capacity of the software to describe complex and different features, classical of HVAC (Heating, Ventilation and Air Conditioning) systems. Interesting conclusions about efficiency are drawn from the comparison, highlighting the potentiality of the software.