AIM: To investigate the histopathologic and morphological changes of the corneas with keratoconus (KC) undergoing penetrating keratoplasty (PKP) according to topographic findings and severity of KC. METHODS: The corneal tissue of 35 samples with KC was retrospectively evaluated with conventional light microscopy. Topographic and pachymetric parameters of keratoconus corneas by means of Pentacam such as mean keratometry (K) and central corneal thickness (CCT) were recorded. Severity of KC was graded according to Amsler-Krumeich classification. RESULTS: Epithelial thinning and breaks in Bowman’s layer are the most common findings in keratoconus corneas (94.3% and 82.9% corneas, respectively). The results revealed statistically significant higher mean K value and lower CCT in the keratoconus corneas that were affected by epithelial thinning, breaks in the Bowman's layer, folds in the Descemet's membrane, epithelial scars, breaks in Descemet's membrane, and stromal scars than those corneas without these findings (P<0.05). Moreover, those corneas with epithelial thinning, breaks in the Bowman's layer, folds in Descemet's membrane, epithelial scars, and stromal scars had significantly more severe disease than those corneas without these findings (P<0.05). The presence of the stromal and epithelial scars were associated with the higher KC severity, in which, respectively, 87.5% and 80.0% of the corneas with stromal and epithelial scars had stage 4 of the KC severity. CONCLUSION: It seems that there are some specific patterns in histologic changes of the keratoconus corneas. The presence of pathologic findings was correlated with thinner and steeper corneas. Epithelial or stromal scars were associated with the highest disease severity. The description of histopathologic findings of KC may help in elucidating the pathogenesis of the disease and help pathologist in differentiating KC from other corneal diseases.