Volatile organic compounds (VOCs) produced by human respiratory cells reflect metabolic and pathophysiological processes which can be detected with the use of modern technology. Analysis of exhaled breath or indoor air may potentially play an important role in screening of upper respiratory tract infections such as COVID-19 or influenza in the future. In this experimental study, air samples were collected and analyzed from the headspace of an in vitro cell culture infected by selected pathogens (influenza A H1N1 and seasonal coronaviruses OC43 and NL63). VOCs were measured with a real-time proton-transfer-reaction time-of-flight mass spectrometer and a differential mobility spectrometer. Measurements were performed every 12 h for 7 d. Non-infected cells and cell culture media served as references. In H1N1 and OC43 we observed four different VOCs which peaked during the infection. Different, individual VOCs were also observed in both infections. Activity began to clearly increase after 2 d in all analyses. We did not see increased VOC production in cells infected with NL63. VOC analysis seems to be suitable to differentiate the infected cells from those which are not infected as well as different viruses, from another. In the future, this could have practical value in both individual diagnostics and indoor environment screening.