BACKGROUND: In infant bronchiolitis, recent evidence indicates that respiratory viruses (e.g., respiratory syncytial virus [RSV], rhinovirus [RV]) contribute to the heterogeneity of disease severity. Of the potential pathobiological molecules, lipids serve as signaling molecules in airway inflammation. However, little is known about the role of the airway lipidome in between-virus heterogeneity and disease severity. METHODS: In this multicenter prospective study of 800 infants hospitalized for RSV or RV bronchiolitis, we analyzed the nasopharyngeal lipidome data. We examined discriminatory lipids between RSV and RV infection and the association of the discriminatory lipids with bronchiolitis severity-defined by positive pressure ventilation (PPV) use. RESULTS: We identified 30 discriminatory nasopharyngeal lipid species and 8 fatty acids between RSV and RV infection. In the multivariable models adjusting for patient-level confounders, 8 lipid species-e.g., phosphatidylcholine (18:2/18:2) (adjOR 0.23, 95%CI 0.11-0.44, FDR=0.0004) and dihydroceramide (16:0) (adjOR 2.17, 95%CI 1.12-3.96, FDR=0.04)-were significantly associated with the risk of PPV use. Additionally, 6 fatty acids-e.g., eicosapentaenoic acid (adjOR 0.27, 95%CI 0.11-0.57, FDR=0.01)-were also significantly associated with the risk of PPV use. CONCLUSIONS: In infants hospitalized for bronchiolitis, the nasopharyngeal lipidome plays an important role in the pathophysiology of between-virus heterogeneity and disease severity.