To examine the corneal collagen cross-linking (CXL) effect with a customized epithelial debridement technique in thin corneas using anterior segment optical coherence tomography (OCT) and confocal microscopy. Two patients with keratoconus who underwent a customized epithelial debridement technique (preserving the epithelium in thinner corneal regions where the deepithelialized corneal thickness was <400 μm) and subsequent CXL were examined by anterior segment OCT and in vivo confocal microscopy 1 month postoperatively. Anterior segment OCT showed the demarcation line in the peripheral deepithelialized corneal areas, but it was not detectable in the central corneal regions corresponding to the cone where the epithelium was preserved. In vivo confocal microscopy analysis revealed total loss of keratocytes together with the intense honeycomb-like stromal edema in the anterior ∼320 μm of the cornea in the deepithelialized areas. This effect was mild under the intact epithelium with preservation of keratocytes and only a mild increase in stromal reflectivity. In this confocal microscopy study, the corneal stroma under the intact epithelium seemed to be spared from the collagen CXL effect by the customized epithelial debridement technique. Copyright 2011, SLACK Incorporated.