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Purpose It's known that severe inflammatory processes may cause limbal stem cell (SC) deficiency decreasing the number of SC niches and changing the microanatomy of these structures. Methods The aim of this study was to evaluate the expression of different SC markers in normal human limbus and to study how an inflammatory conditions can modulate these antigens. To understand the pathological changes in limbal crypts structure due to severe inflammation, a case of corneal melting and perforation in advanced herpes simplex (HSV) disease, two cases of endophthalmitis and a case of fungal infection were analyzed.Samples were examined by immunohistochemistry or immunofluorescence for p63, vimentin, laminin5, integrin (Int) α6, int β1, int β4, ABCG2, desmoglein 3, connexin43, N‐cadherin and cytokeratin (K) 12 positivity. We evaluated the anatomical structure of limbal crypts in each case and the positivity for SC marker used to identify SC. Results In normal limbus, the investigated SC markers were positive. In the HSV we didn't observe presence of crypts, whereas in both cases of endophthalmitis crypts were still present but they had an atypical structure: the basal cells in the crypts were "stretched" and endowed by inflammatory cells. In the pathological cases, we observed positivity for K12 while, among SC markers, p63, ABCG2 and connexin43 were still present; the others antigens were variably expressed. Conclusion Different pathologies involving the limbus may result in marked chenges of expression of SC markers within the crypts. [ABSTRACT FROM AUTHOR]