The differential diagnosis includes oral lichen planus, erythematous candidiasis, leukoplakia, lupus erythematosus, glossitis, and chemical burns. Atrophic glossitis is usually distinguished from benign migratory glossitis on the basis of the migrating pattern of the lesions and the presence of a whitish border, features which are not present in atrophic glossitis, which instead shows lesions which enlarge rather than migrate. Rarely, blood tests may be required to distinguish from glossitis associated with anemia or other nutritional deficiencies. Since the appearance and the history of the condition (i.e. migrating areas of depapillation) are so striking, there is rarely any need for biopsy. When biopsy is taken, the histopathologic appearance is quite similar to psoriasis:

Hyperparakeratosis. Acanthosis. Subepithelial T lymphocyte inflammatory infiltrate. Migration of neutrophilic granulocytes into the epithelial layer, which may create superficial microabscesses, similar to the Munros microabscesses described in pustular psoriasis. Classification
Geographic tongue could be considered to be a type of glossitis. It usually presents only on the dorsal 2/3 and lateral surfaces of the tongue, but less commonly an identical condition can occur on other mucosal sites in the mouth, such as the ventral surface (undersurface) of the tongue, mucosa of the cheeks or lips, soft palate or floor of mouth; usually in addition to tongue involvement. In such cases, terms such as stomatitis erythema migrans, ectopic geographic tongue, areata migrans, geographic stomatitis, or migratory stomatitis are used instead of geographic tongue.
Pseudostrabismus is the false appearance of crossed eyes. When the eyes are actually crossed or not completely aligned with one another, it is called strabismus. Pseudostrabismus is more likely to be observed in East Asian or Native American infants, due to the presence of epicanthic folds obscuring the medial aspect of each eye. Pseudostrabismus generally occurs in infants and toddlers, whose facial features are not fully developed. The bridge of their nose is wide and flat, creating telecanthus (increased distance between medial canthus of both eyes). With age, the bridge will narrow, and the epicanthic folds in the corner of the eyes will go away. This will cause the eyes to appear wider and thus not have the appearance of strabismus. To detect the difference between strabismus and pseudostrabismus, clinicians use a flashlight to shine into the childs eyes. When the child is looking at the light, a reflection can be seen on the front surface of the pupil. If the eyes are aligned with one another, the reflection from the light will be in the same spot of each eye. If strabismus is present, the reflection from the light will not be in the same spot of each eye. Rakels Textbook of Family Medicine states, "A common misconception is that children with crossed eyes outgrow the condition, but this is generally not the case. This belief stems from the confusion between true strabismus and pseudostrabismus.