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Background- The malignancy of the oral cavity constitutes the most important group of malignancies in South and Southeast Asia.The risk increases with the use of tobacco products. Materials & Methods- Micronuclei frequency scoring was used as a biomarker to identify different potentially malignant disorders. Results- Mean micronuclei index was found higher using Hematoxylin and Eosin stain than Papanicolaou's stainand May Grunwald's stain. Conclusion- We concluded that the micronuclei frequencies in oral exfoliated epithelial cells using three different stains- Hematoxylin and Eosin stain, Papanicolaou's stain, May Grunwald's stain may be useful in predicting the malignant potential of premalignant lesions.