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We aimed to elucidate the molecular pathways associated with fluorescence properties of oral potentially malignant disorders (OPMD) visualised under direct tissue autofluorescence (VELscope™).Forty-two oral mucosal biopsies correlated with clinical fluorescence characteristics were categorised based on histopathological diagnosis. Four oral squamous cell carcinoma (OSCC), 15 oral epithelial dysplasia (OED), nine oral lichen planus (OLP) and 14 oral epithelial hyperplasia (OEH) presenting with three fluorescence patterns including retained fluorescence (RF), loss of fluorescence (LAF) with blanching (LB) and LAF with no blanching (LNB) were assessed. Relative gene expression was measured through RNA sequencing.Although each lesion type had a specific set of histology-related differentially expressed genes (DEGs), all tested samples shared a number of DEGs, and we could not identify a discriminatory component between histological groups. Gene ontology enrichment revealed LAF in OEH was mostly due to changes in inflammation, cell cycle regulation and apoptosis, while in OED was due to inflammation, angiogenesis and extracellular matrix remodelling. Inflammatory reactions were associated with diascopic fluorescence (DF) for both OEH and OED.Uncovering the molecular mechanisms underlying LAF and DF may lead to reduction in the number of false-positive and false-negative findings and improve the efficacy and utility of VELscope™.