A system for preventing cross-contamination in single-limb ventilators is described. In one embodiment, the system includes an airflow generator connected in-line to a humidifier, a first check valve and a patient interface by a gas flow circuit. A controller is electrically coupled to the airflow generator, and a cartridge is connected to the gas flow circuit between a first point downstream of the humidifier and a second point upstream of the patient interface. The cartridge includes a bacteria filter and the first check valve. A method for preventing cross-contamination in single-limb ventilators and a method for providing gaseous flow through a single-limb ventilator are also described.