Due to the subjective nature of autotopagnosia, there are many hypotheses presented as to the underlying causation. Since the condition by definition is an inability to recognize the human body and its parts, the disorder could stem from a language deficit specific to body parts. On the other hand, the patient could suffer from a disrupted body image or a variation of the inability to separate parts from whole. It is also believed that autotopagnosia has multiple underlying causes that cannot be categorized as either language-specific or body-image-specific. The rarity of autotopagnosia, frequently combined with the manifestation of other psychoneurological disorders, makes the prime cause extremely difficult to study. In many cases, one of these accompanying conditions—often aphasia—could be masking the patient’s autotopagnosia altogether.

Autotopagnosia from the Greek "a" and "gnosis," meaning "without knowledge", "topos" meaning "place", and "auto" meaning "oneself", autotopagnosia virtually translates to the "lack of knowledge about one's own space," and is clinically described as such.

Autotopagnosia is a form of agnosia, characterized by an inability to localize and orient different parts of the body. The psychoneurological disorder has also been referred to as "body-image agnosia" or "somatotopagnosia." "Somatotopagnosia" has been argued to be a better suited term to describe the condition. While autotopagnosia emphasizes the deficiencies in localizing only one's own body parts and orientation, "somatotopagnosia" also considers the inability to orient and recognize the body parts of others or representations of the body (e.g., manikins, diagrams).

Typically, the cause of autotopagnosia is a lesion found in the parietal lobe of the left hemisphere of the brain. However, it as also been noted that patients with generalized brain damage present with similar symptoms of autotopagnosia.

As a concept, autotopagnosia has been criticized as nonspecific; some claim that this is a manifestation of a greater symptomatic complex of anomia, marked by an inability to name things in general—not just parts of the human body.