Although sometimes referred to as 'simple microphthalmia', nanophthalmia is a condition in which the size of the eye is small but no anatomical alterations are present.

[3] The presence of a small eye within the orbit can be a normal incidental finding but in many cases it is atypical and results in visual impairment.

[3][1][6] It has been postulated that microphthalmia arises as a result of interference with postnatal eye growth, in contrast to anophthalmia which originates much earlier during fetal development.

[3][7] Microphthalmia in newborns is sometimes associated with fetal alcohol spectrum disorder[2] or infections during pregnancy, particularly herpes simplex virus, rubella and cytomegalovirus (CMV), but the evidence is inconclusive.

In mammals, the failure of expression of MITF in the retinal pigment epithelium prevents this structure from fully differentiating, causing a malformation of the choroid fissure of the eye and drainage of vitreous body fluid.

The identification of the genetics of WS type 2 owes a lot to observations of phenotypes of MITF-mutant mice.

[3] An ultrasound may also be conducted to confirm whether the axial length of the eye is clinically below average (i.e. at least 2 standard deviations below the age-adjusted mean).

The small orbit size characteristic of microphthalmia can impact the growth and structural development of the face after birth.

[13] An axial length of less than 16 mm (0.63 in) indicates that a microphthalmic eye's growth will not be sufficient, and intervention will be necessary to reduce the degree of facial asymmetry.

[5][13] Typically, an infant begins wearing a conformer, or an unpainted ocular prosthesis, in the first weeks of life.

[13] If the microphthalmic eye has functional vision, an affected individual may opt against wearing a painted prothesis.