Unequal pupils may indicate physiologic anisocoria, a birth defect; drugs used to treat other eye conditions; or neurological conditions that affect the third cranial nerve, according to The Merck Manual Home Edition. Disorders in the brain that affect the pupils include strokes, bleeding in the brain, infections or tumors.
Physiologic anisocoria is marked by pupils that appear naturally different in size. This condition occurs in 20 percent of the population, and the difference in sizes does not affect how people see. Pupils affected by physiologic anisocoria react to light normally, notes The Merck Manual Home Edition. Eye disorders and drugs used to treat them may cause unequal pupil sizes. Homatropine is used for inflammation of the eye, and pilocarpine treats glaucoma. Both of these drugs may cause pupils to have different sizes. Iritis, or inflammation of the eye, and glaucoma can also make the pupils become unequal.
Strokes and brain hemorrhaging can affect the pathways of the cranial nerves that control muscles and actions of the eye. Brain disorders such as tumors and infections can also affect the pupil sizes, but these are not as common as strokes and bleeding, explains The Merck Manual Home Edition. Other symptoms may be a cause for concern if they appear alongside unequal pupils. These symptoms include droopy eyelids, double vision, loss of vision, headache and eye pain and could be warning signs of a more serious medical condition in the brain.