Analysis of samples of exhaled breath condensate (EBC) is a promising noninvasive method for the control of the status of the human respiratory system. In the present work, the proteome of the EBC samples received from a patient with lung dystrophy at different times before and after bilateral lung transplantation is analyzed by ion cyclotron resonance mass spectrometry. Qualitative protein composition of EBC samples obtained during the first month correlates with the clinical data on the acceptance of the transplanted lungs (allograft). Fifteen months after the lung surgery, the protein spectrum was similar to the normal composition of EBC proteins. This result agrees with the medical conclusion about normal lung functioning. The results suggest that the mass spectrometric monitoring of the protein spectra of EBC may be a tool for noninvasive pulmonological diagnostics.