Breath analysis systems and methods test for infectious diseases in exhaled breath gas or condensate. An automatic breath sampling system can obtain reliable samples over a variety of clinical situations. In some variations, the system is modular system and can protect the equipment and clinician from contamination. In some variations, the system can be a point-of-care rapid-result instrument. In some variations, can be configured for off-line analysis in which case the collected sample is presented to a stand-alone analyzer for measurement.