BACKGROUND: As treatment responses differ according to the inflammatory endotype of chronic rhinosinusitis (CRS), identifying the endotype could facilitate personalized treatment. We aimed to identify a noninvasive epithelial lining fluid (ELF) biomarker for the type 2 (T2) endotype of CRS. METHODS: Nasal tissue and ELF samples were obtained from patients with CRS and control individuals. Single-cell RNA sequencing (scRNA-seq) data were analyzed. The expression of inflammatory mediators was measured using Luminex multiplex assays and enzyme-linked immunosorbent assays. RESULTS: Analysis of the scRNA-seq data revealed that CST1 was exclusively expressed in epithelial cells of T2 CRS, but not in those of non-T2 CRS, and this was confirmed by immunofluorescence staining. Cystatin SN expression was detected in ELF, and its levels were significantly higher in T2 CRS than in non-T2 CRS and controls. The expression level of cystatin SN in the ELF was positively correlated with the Lund-Mackay CT, SNOT-22, and JESREC scores, whereas it was inversely correlated with olfactory function. Furthermore, ELF cystatin SN levels correlated with the tissue/blood eosinophil count and nasal tissue expression of T2 inflammatory mediators, indicating that ELF cystatin SN is a reliable marker of nasal T2 inflammation. In the receiver operating characteristics curve analysis evaluating the predictive efficacy for T2 CRS, the AUC for ELF cystatin SN was 0.894 (0.936 in the validation cohort), which was higher than that of other markers, including blood eosinophil count, serum total IgE level, and the JESREC score. With a cut-off value of 112.5 ng/mg, ELF cystatin SN yielded a 75.0% sensitivity and 92.0% specificity. CONCLUSIONS: ELF cystatin SN is a clinically feasible, noninvasive biomarker with superior accuracy for predicting T2 CRS.