An effective design of the ventilation system of the isolation rooms for infectious patients can reduce the risk of spreading infections. However, no consensus exists regarding the placement of the air inlets and outlets which minimises the risk of spreading infection. In this work, we use computational fluid dynamics (CFD) to evaluate the ability of the ventilation system to minimise the risk of infection in the rooms of isolated infectious patients. We analyse the influence of the position of the air inlets and outlets. We take into account the deposition and viability of the infectious particles. To compare the different configurations quantitatively, three types of indices are employed: those which quantify the capacity to renew the air; those which quantify the capacity to remove a contaminant and those which quantify the risk of airborne infection. These three types of indices are applied to the entire isolation room and in specific zones of the room in order to evaluate the quality of the ventilation globally and locally respectively. Likewise, using different air diffusers we demonstrate the importance of the diffuser on the air flow pattern and, therefore, on the quality of the ventilation.