Background: Oral squamous cell carcinoma (OSCC) is still one of the most common lethal malignancies of the oral cavity. One of the reasons for its treatment failure is thought to be related to the presence of a subpopulation of cells within the tumor called cancer stem cells (CSCs). CSCs display stem cell-like characteristics that impart resistance to conventional treatment modalities and promote tumor initiation, progression, and metastasis. Specific markers for this population have been investigated in the hope of developing a deeper understanding of their role in the pathogenesis of OSCC and elucidating novel therapeutic strategies. Over the past years, different techniques and markers have been investigated. Cripto-1(CR-1) is an identified oncogene which was overexpressed in a wide spectrum of human malignant solid tumours, introducing a potential therapeutic target for human cancers and was significantly associated with initiation and aggressiveness of human cancers. Methods: In this study 40 samples of well and poorly differentiated squamous cell carcinoma were obtained to study the difference of cripto-1 expression according to the degree of differentiation using the immunofluorescent technique. Results: CR-1 was over expressed in well differentiated samples compared to poorly differentiated samples and immunofluorescent expression showed significant decrease in mean percentage (P˂ 0.05). Conclusion: CSCs has a role in initiation and progression of OSCC and CR-1 can be considered as a good marker for detection of these cells.