Background: Leukoplakia, is a precancerous lesion that is most commonly encountered in the oral cavity. The grade of dysplasia is presumed to be the most important indicator of malignant potential. There are many promising aspects in advanced methods for the evaluation of oral precancer and cancer. Among these methods, electron microscopic examination predicts the true biologic potential more accurately than conventional histology and has some success in the early detection of potentially malignant lesions. It has been reported in the literature that there is some correlation between clinical, histopathological, and transmission electron microscopic features. Materials and Methods: In this cohort study (prospective research), from the total of 9 subjects, 3 had homogenous leukoplakia, 3 had ulcerative type of oral leukoplakia, and 3 had nodular type of oral leukoplakia. Two patients were selected as control patients. Transmission electron microscopic examination was carried for all the cases and controls. All the findings were correlated with clinical features and light microscopy. Results: Clinically and histologically, mild leukoplakia showed break in basement membrane, which can only be observed under transmission electron microscope (TEM). Additional dysplastic features were observed under transmission electron microscope, which are indicative of neoplastic process. Conclusions: Thus, it is finally concluded that nodular leukoplakia seems to be the most severe clinical type of leukoplakia showing highest risk of malignant transformation. Homogenous leukoplakia might show break in basement membrane under TEM.