To investigate intravital morphological features of the broader area of the lingual mucosa in clinically healthy subjects, and to attempt to evaluate subclinical conditions, we evaluated detailed intravital morphological features of the lingual mucosa using our newly developed oral contact mucoscopy techniques. Clinically healthy subjects (female: 19–22 years, average age: 20.27 years, and n?=?28) were enrolled. A position indicator stain was placed on the lingual mucosal surface, and sliding images were captured and then reconstructed. In addition, the lingual mucosa was divided into six areas, and morphometry of the fungiform and filiform papillae was performed. The results were statistically analyzed. There were two morphological features among clinically healthy subjects involving the filiform papillae: the length of the papillae and the degree of biofilm (tongue coat) deposition. We defined a modified tongue coat index (mTCI) with scores ranging from 0 (tongue coating not visible) to 0.5, 1, 1.5, and 2 (thick tongue coating) for six sections of the tongue dorsum. No subjects received a score of 2. Significant differences were found in the mTCI between the six sections of the tongue dorsum, especially between the posterior areas and the lingual apex. The fungiform papillae of some subjects exhibited elongated morphological changes. Our findings suggest that magnified lingual dorsum examination of a broader area is especially important in accurate screening for subclinical or transient conditions of potential lingual mucosal diseases. For this purpose, our new oral mucoscopy and non-invasive intravital observational techniques were especially effective.