<b><i>Background:</i></b> Eradication of malignant tumors at the primary site with oncological safe margin is a critical requirement for obtaining better survival rate and less recurrence. Touch imprint cytology (TIC) has proven itself as a quick, simple, inexpensive, highly accurate and reliable intraoperative technique to assess surgical margins in squamous cell carcinomas of the oral cavity. However, it is still unclear how the mode of excision, i.e. by scalpel (SC) and electrocautery (EC), or the method of staining, i.e. Papanicolaou (PAP) and cytohaem, affect the diagnostic accuracy of TIC. <b><i>Objective:</i></b> To study the influence of confounding factors like mode of excision (EC/SC) and staining (PAP/cytohaem) on the diagnostic accuracy of intraoperative TIC technique for assessing surgical margins in oral squamous cell carcinoma in comparison to paraffin-embedded HE-stained sections. <b><i>Materials and Methods:</i></b> Thirty patients underwent surgical treatment for primary oral squamous cell carcinoma. Three hundred and forty-eight touch imprint slides were prepared from 174 margins of 30 resected tumor specimens. Two adjacent tissues from the margin to be evaluated were imprinted to observe differences between surfaces excised by EC and SC. The set of imprint from each margin tissue was stained with PAP and cytohaem. The TIC results of 180 EC-excised margins and 168 SC-excised margins were compared. Results of 174 imprints stained with RAPID-PAP were compared to their counterpart comprising of 174 cytohaem-stained imprints. The slides were diagnosed as positive, negative or suspicious for tumor. Finally, TIC results were checked against their respective histopathological sections. <b><i>Results:</i></b> No statistically significant difference was found between the results of imprints from EC/SC-excised margins (Z = 0.44, p = 0.70) or the imprints stained with PAP/cytohaem (Z = 0.44, p = 0.70). <b><i>Conclusion:</i></b> Confounding factors like mode of excision and staining procedure do not significantly influence the results of imprint cytology.