The bronchoalveolar lavage (BAL) and its cells have been widely used as a support for clinical diagnosis and as a versatile tool for research questions since many years. Because there are no sufficient possibilities of long-term storage, the authors explore in this study the utility of a new fixative for fixation and paraffin embedding of human lavage cells with the possibility of implementing standard molecular biology techniques. HOPE-fixed, paraffin-embedded BAL cells of patients with different lung diseases (asthma, chronic obstructive pulmonary diseases, tuberculosis, sarcoidosis, emphysema, and fibrosis) were subjected to immunohistochemistry, in situ hybridization, quantitative polymerase chain reaction, and transcription microarray analysis. Furthermore, two-dimensional gel electrophoresis was conducted to evaluate the range of possible applications for research, diagnostics, and further implementing in biobanks. The authors show, by targeting some exemplary molecules, the power of screening and validating HOPE-BAL for new biomarkers. The transforming growth factor β signaling pathway may play a central role in immunomodulation upon infection as well as asthma. Furthermore, haptoglobin was overexpressed in asthma and sarcoidosis. Because of the excellent preservation of nucleic acids, protein, and morphologic structures, HOPE-BAL is a step forward into enhanced molecular diagnostics and biobanking in pulmonary medicine.