Conjunctival epithelial lesions vary from benign to borderline malignancy to malignant, therefore it is extremely important to detect the molecular markers of the malignant progression of conjunctival intraepithelial lesions. The aim of our study was to analyse the molecular markers of the progression of conjunctival intraepithelial lesions. We have analysed Ki67, PHH3, Bcl2, P53, P63 and CK7 using standard immunohistochemistry. In addition, we have calculated the squamous-glandular index based on the evaluation of H&E stained specimens and as the ratio of P63/CK7. The results of our study indicated that the presence of squamous epithelium is significantly increased during the progression of conjunctival intraepithelial lesions, and therefore the squamous-glandular index is also increased. In addition, it is possible to divide conjunctival intraepithelial lesions as low grade and high grade lesions based on the distribution of proliferation and apoptosis markers.