BACKGROUND This case report illustrates the incidental detection of atypical hyporeflective bleb-like structures in an otherwise asymptomatic human cornea, highlighting the effectiveness of non-invasive biophotonic imaging techniques such as optical coherence tomography (OCT) and large-area confocal laser scanning microscopy (CLSM). CASE REPORT A 57-year-old man underwent a comprehensive ophthalmological examination, including slit-lamp biomicroscopy, corneal topography, and densitometry, as part of a clinical study. The patient presented with a clear cornea, a deep and optically empty anterior chamber, and a clear crystalline lens in both eyes. Best-corrected distance visual acuity was -0.1 logMAR. He denied ocular pain, tearing, or photophobia. There was no history of ocular trauma, infectious or genetic diseases, or ocular surgery. Further, OCT and large-area CLSM were employed for a more in-depth analysis of the corneal structure. Standard ophthalmological assessments indicated normal ocular health with no apparent corneal abnormalities. High-resolution OCT and large-area CLSM imaging revealed atypical hyporeflective bleb-like structures within the corneal epithelium and sub-basal nerve plexus but not in the stroma. CONCLUSIONS The authors hypothesize that the observed findings may indicate an early stage of epithelial basement membrane dystrophy, potentially preceding the manifestation of clinical symptoms, detectable solely through advanced biophotonic imaging methods. It is important to emphasize that these observations do not represent a definitive diagnosis. Nevertheless, the discovery of these atypical structures via advanced imaging underscores the importance of incorporating non-invasive biophotonic techniques into preoperative eye examinations in certain situations. This approach could significantly improve the early detection and management of corneal diseases, leading to improved patient outcomes.