The complex interaction between cancer cells and the microenvironment plays an essential role in all stages of tumourigenesis. Despite the significance of this interplay, alterations in protein composition underlying tumour-stroma interactions are largely unknown. The aim of this study was to identify stromal proteins with clinical relevance in non-small cell lung cancer (NSCLC). A list encompassing 203 stromal candidate genes was compiled based on gene expression array data and available literature. The protein expression of these genes in human NSCLC was screened using the Human Protein Atlas. Twelve proteins were selected that showed a differential stromal staining pattern (BGN, CD99, DCN, EMILIN1, FBN1, PDGFRB, PDLIM5, POSTN, SPARC, TAGLN, TNC and VCAN). The corresponding antibodies were applied on tissue microarrays, including 190 NSCLC samples, and stromal staining was correlated with clinical parameters. Higher stromal expression of CD99 was associated with better prognosis in the univariate (p 5 0.037) and multivariate (p 5 0.039) analysis. The association was independent from the proportion of tumour stroma, the fraction of inflammatory cells and clinical and pathological parameters like stage, performance status and tumour histology. The prognostic impact of stromal CD99 protein expression was confirmed in an independent cohort of 240 NSCLC patients (p 5 0.008). Furthermore, double-staining confocal fluorescence microscopy showed that CD99 was expressed in stromal lymphocytes as well as in cancer-associated fibroblasts. Based on a comprehensive screening strategy the membrane protein CD99 was identified as a novel stromal factor with clinical relevance. The results support the concept that stromal properties have an important impact on tumour progression.Non-small cell lung cancer (NSCLC) represents the leading cause of cancer-related death world-wide. 1 Despite advances in NSCLC management, the effectiveness of available treatments is limited and the general prognosis remains poor. Although clinically important molecular biomarkers, like epidermal growth factor receptor mutations and ALK-EML4 translocations, have been identified in subgroups of patients, 2,3 the failure of long-lasting therapy responses and the absence of other valuable biological targets stress the need for new treatment strategies.NSCLC is a heterogeneous entity, comprising defined histological subtypes of adenocarcinoma, squamous cell carcinoma and large cell cancer, each with distinguishing morphological features. However, the stromal cell compartment in lung cancer is characterised by a common desmoplastic