Stem cells represent the small subpopulation of healthy and cancerous tissues, which are characterised with increased proliferation and self-renewal properties. From the many different markers of stem cells, we have investigated the stem cell index during the progression of cervical intraepithelial neoplasia (CIN), based on the immunohistochemical expression of CD44 in total of 140 tissue samples from uterine cervix. In addition, we have performed the profound correlation analysis of CD44 with different epithelial-mesenchymal, proliferation, apoptosis and hormonal markers at both protein and mRNA level. The results of our study indicated that, stem cell index based on the CD44 detection is significantly increased with the progression of cervical intraepithelial neoplasia. In addition, CD44 expression significantly correlates with the epithelial-mesenchymal transition, proliferation-apoptotic features and ER status in both protein and mRNA level. Two, groups of cervical intraepithelial lesions as well as carcinoma can be identified based on the expression of CD44, Ki67, Cas3 and ER. To the best of our knowledge we are first to demonstrate such findings in CIN and cervical carcinoma and identified characteristics could be used for the early assessment of CIN patient prognosis and for the relevant clinical management.