The identification of chemical compounds in exhaled human breath is promising in the search for new biomakers of diseases. However, the analytical techniques used nowadays are not capable of achieving a robust identification, especially in real-time analysis. In this work, we show that real-time high-resolution tandem mass spectrometry (HRMS/MS) is suitable for the identification of biomarkers in exhaled breath. Using this approach, we identified a number of furan derivatives, compounds found in the exhalome whose nature and origin are not yet clearly understood. It is also shown that the combination of HRMS/MS with UHPLC allowed not only the identification of the furan derivatives but also the proper separation of their isomeric forms.