Background: Presence of micronuclei in cells is a reflection of structural and chromosomal aberration in cells. Micronuclei frequency has been proved to be a reliable marker of genomic damage and can be applied to buccal cell cytology to determine the susceptibility. This method may help monitor and predict increased risk of cancer in humans. Aim: The present study aims to determine micronuclei frequency in control, oral submucous fibrosis (OSMF) and oral squamous cell carcinoma (OSCC) patients in oral cytology specimens and compare the efficiency of Papanicolaou (PAP) and May-Grunwald Giemsa (MGG) staining techniques for same. Materials and methods: Study groups consisted of 100 patients each of control, OSMF and OSCC. Two smears were obtained from each patient, each of which was stained with PAP and MGG stain. A total of 100 cells were evaluated for micronuclei in each slide using Tolbert’s criteria and micronuclei frequency was calculated. Results: The mean micronuclei frequency was higher in the PAP stained smears in all the three groups than in the MGG stained smears and is the preferred staining method. Multiple comparisons between the three groups showed that MN frequency increased step-wise from control to OSMF to OSCC group of patients. Conclusion: Oral cytology is the least invasive and inexpensive method for measuring DNA damage and can be used as a field test using PAP stain. It can be used as a marker for epithelial precancer (OSMF) and cancer progression.