An automatic breath collecting and sampling system, which is preferably carried by the subject, or otherwise kept with him or near him, for the recommended duration of the collection period. The system collects samples in separate switchable containers, either at predetermined time intervals, or in response to an automatic stimulus, which could be related to the breath content itself, or to another physiological signal, such as the subject s pulse rate, breath rate, blood pressure, or temperature, or in response to a signal related to an environmental effect, such as the presence of a strong concentration in the air of a foreign gas, which could be detected by an electrochemical sensor, or manually by the subject after being prompted by the system. After collection of the requisite number of separate containers, they may be detached and sent for analysis or other treatment.