Other causes of color blindness include brain or retinal damage caused by shaken baby syndrome, accidents and other trauma which produce swelling of the brain in the occipital lobe, and damage to the retina caused by exposure to ultraviolet light (10–300 nm). Damage often presents itself later on in life.

Color blindness may also present itself in the spectrum of degenerative diseases of the eye, such as age-related macular degeneration, and as part of the retinal damage caused by diabetes. Another factor that may affect color blindness includes a deficiency in Vitamin A.

Some subtle forms of colorblindness may be associated with chronic solvent-induced encephalopathy (CSE), caused by longtime exposure to solvent vapors.

Red–green color blindness can be caused by ethambutol, a drug used in the treatment of tuberculosis.

Color blindness is typically inherited. It is most commonly inherited from mutations on the X chromosome but the mapping of the human genome has shown there are many causative mutations—mutations capable of causing color blindness originate from at least 19 different chromosomes and 56 different genes (as shown online at the Online Mendelian Inheritance in Man (OMIM)).

Two of the most common inherited forms of color blindness are protanomaly (and, more rarely, protanopia – the two together often known as "protans") and deuteranomaly (or, more rarely, deuteranopia – the two together often referred to as "deutans").

Both "protans" and "deutans" (of which the deutans are by far the most common) are known as "red–green color-blind" which is present in about 8 percent of human males and 0.6 percent of females of Northern European ancestry.

Some of the inherited diseases known to cause color blindness are:

- cone dystrophy

- cone-rod dystrophy

- achromatopsia (a.k.a. rod monochromatism, stationary cone dystrophy or cone dysfunction syndrome)

- blue cone monochromatism (a.k.a. blue cone monochromacy or X-linked achromatopsia)

- Leber's congenital amaurosis

- retinitis pigmentosa (initially affects rods but can later progress to cones and therefore color blindness).

Inherited color blindness can be congenital (from birth), or it can commence in childhood or adulthood. Depending on the mutation, it can be stationary, that is, remain the same throughout a person's lifetime, or progressive. As progressive phenotypes involve deterioration of the retina and other parts of the eye, certain forms of color blindness can progress to legal blindness, i.e., an acuity of 6/60 (20/200) or worse, and often leave a person with complete blindness.

Color blindness always pertains to the cone photoreceptors in retinas, as the cones are capable of detecting the color frequencies of light.

About 8 percent of males, and 0.6 percent of females, are red-green color blind in some way or another, whether it is one color, a color combination, or another mutation. The reason males are at a greater risk of inheriting an X linked mutation is that males only have one X chromosome (XY, with the Y chromosome carrying altogether different genes than the X chromosome), and females have two (XX); if a woman inherits a normal X chromosome in addition to the one that carries the mutation, she will not display the mutation. Men do not have a second X chromosome to override the chromosome that carries the mutation. If 8% of variants of a given gene are defective, the probability of a single copy being defective is 8%, but the probability that two copies are both defective is 0.08 × 0.08 = 0.0064, or just 0.64%.

There is generally no treatment to cure achromatopsia. However, dark red or plum colored filters are very helpful in controlling light sensitivity.

Since 2003, there is a cybernetic device called eyeborg that allows people to perceive color through sound waves. Achromatopsic artist Neil Harbisson was the first to use such a device in early 2004, the eyeborg allowed him to start painting in color by memorizing the sound of each color.

Moreover, there is some research on gene therapy for animals with achromatopsia, with positive results on mice and young dogs, but less effectiveness on older dogs. However, no experiments have been made on humans. There are many challenges to conducting gene therapy on humans. See Gene therapy for color blindness for more details about it.

Acquired achromatopsia/dyschromatopsia is a condition associated with damage to the diencephalon (primarily the thalamus of the mid brain) or the cerebral cortex (the new brain), specifically the fourth visual association area, V4 which receives information from the parvocellular pathway involved in colour processing.

Thalamic achromatopsia/dyschromatopsia is caused by damage to the thalamus; it is most frequently caused by tumor growth since the thalamus is well protected from external damage.

Cerebral achromatopsia is a form of acquired color blindness that is caused by damage to the cerebral cortex of the brain, rather than abnormalities in the cells of the eye's retina. It is most frequently caused by physical trauma, hemorrhage or tumor tissue growth.

In segmental heterochromia, sometimes referred to as sectoral heterochromia, areas of the same iris contains two completely different colors.

Segmental heterochromia is rare in humans; it is estimated that only about 1% of the population have it.

Heterochromia has also been observed in those with Duane syndrome.

Hemeralopia is known to occur in several ocular conditions. Cone dystrophy and achromatopsia, affecting the cones in the retina, and the anti-epileptic drug Trimethadione are typical causes. Adie's pupil which fails to constrict in response to light; Aniridia, which is absence of the iris; Albinism where the iris is defectively pigmented may also cause this. Central Cataracts, due to the lens clouding, disperses the light before it can reach the retina, is a common cause of hemeralopia and photoaversion in elderly. C.A.R (Cancer Associated Retinopathy) seen when certain cancers incite the production of deleterious antibodies against retinal components, may cause hemeralopia.

Another known cause is a rare genetic condition called Cohen Syndrome (aka Pepper Syndrome). Cohen syndrome is mostly characterized by obesity, mental retardation, and craniofacial dysmorphism due to genetic mutation at locus 8q22-23. Rarely it may have ocular complications such as hemeralopia, pigmentary chorioretinitis, optic atrophy or retinal/iris coloboma, having a serious effect on the person's vision.

Yet another cause of hemeralopia is uni- or bilateral postchiasmatic brain injury. This may also cause concomitant night blindness.

Hemeralopia (from Greek "ημέρα", hemera "day"; and "αλαός", alaos "blindness") is the inability to see clearly in bright light and is the exact opposite of nyctalopia (night blindness). Hemera was the Greek goddess of day and Nyx was the goddess of night. However, it has been used in an opposite sense by many non-English-speaking doctors. It can be described as insufficient adaptation to bright light. It is also called heliophobia and day blindness.

In hemeralopia, daytime vision gets worse, characterised by photoaversion (dislike/avoidance of light) rather than photophobia (eye discomfort/pain in light) which is typical of inflammations of eye. Nighttime vision largely remains unchanged due to the use of rods as opposed to cones (during the day), which are affected by hemeralopia and in turn degrade the daytime optical response. Hence many patients feel they see better at dusk than in daytime.

Causes of photophobia relating directly to the eye itself include:

- Achromatopsia

- Aniridia

- Anticholinergic drugs may cause photophobia by paralyzing the iris sphincter muscle.

- Aphakia (absence of the lens of the eye)

- Blepharitis

- Buphthalmos (abnormally narrow angle between the cornea and iris)

- Cataracts

- Coloboma

- Cone dystrophy

- Congenital abnormalities of the eye

- Viral conjunctivitis ("pink eye")

- Corneal abrasion

- Corneal dystrophy

- Corneal ulcer

- Disruption of the corneal epithelium, such as that caused by a corneal foreign body or keratitis

- Ectopia lentis

- Endophthalmitis

- Eye trauma caused by disease, injury, or infection such as chalazion, episcleritis, glaucoma, keratoconus, or optic nerve hypoplasia

- Hydrophthalmos, or congenital glaucoma

- Iritis

- The drug isotretinoin (Accutane/Roaccutane) has been associated with photophobia

- Optic neuritis

- Pigment dispersion syndrome

- Pupillary dilation (naturally or chemically induced)

- Retinal detachment

- Scarring of the cornea or sclera

- Uveitis

X-linked congenital stationary night blindness (CSNB) is a rare X-linked non-progressive retinal disorder. It has two forms, complete, also known as type-1 (CSNB1), and incomplete, also known as type-2 (CSNB2), depending on severity. In the complete form (CSNB1), there is no measurable rod cell response to light, whereas this response is measurable in the incomplete form. Patients with this disorder have difficulty adapting to low light situations due to impaired photoreceptor transmission. These patients also often have reduced visual acuity, myopia, nystagmus, and strabismus. CSNB1 is caused by mutations in the gene NYX, which encodes a protein involved in retinal synapse formation or synaptic transmission. CSNB2 is caused by mutations in the gene CACNA1F, which encodes a voltage-gated calcium channel Ca1.4.

Not all Congenital Stationary Night Blindness (CSNB) are inherited in X-linked pattern. There are also dominant and recessive inheritance patterns for CSNB.

Patients may develop photophobia as a result of several different medical conditions, related to the eye or the nervous system. Photophobia can be caused by an increased response to light starting at any step in the visual system, such as:

- Too much light entering the eye. Too much light can enter the eye if it is damaged, such as with corneal abrasion and retinal damage, or if its pupil(s) is unable to normally constrict (seen with damage to the oculomotor nerve).

- Due to albinism, the lack of pigment in the colored part of the eyes (irises) makes them somewhat translucent. This means that the irises can't completely block light from entering the eye.

- Overstimulation of the photoreceptors in the retina

- Excessive electric impulses to the optic nerve

- Excessive response in the central nervous system

- Elevated trigeminal nerve tone (as it is sensory nerve to eye, elevated tone makes it over reactive). Elevated trigeminal tone causes elevated substance P which causes hypersensitivity. Often due to jaw misalignment.

Common causes of photophobia include migraine headaches, TMJ, cataracts, Sjogren's Syndrome, Mild Traumatic Brain Injury (MTBI), or severe ophthalmologic diseases such as uveitis or corneal abrasion. A more extensive list follows:

The X-linked varieties of congenital stationary night blindness (CSNB) can be differentiated from the autosomal forms by the presence of myopia, which is typically absent in the autosomal forms. Patients with CSNB often have impaired night vision, myopia, reduced visual acuity, strabismus, and nystagmus. Individuals with the complete form of CSNB (CSNB1) have highly impaired rod sensitivity (reduced ~300x) as well as cone dysfunction. Patients with the incomplete form can present with either myopia or hyperopia.

Cerebral achromatopsia differs from other forms of color blindness in subtle but important ways. It is a consequence of cortical damage that arises through ischemia or infarction of a specific area in the ventral occipitotemporal cortex of humans. This damage is almost always the result of injury or illness.

Cerebral achromatopsia is a type of color-blindness caused by damage to the cerebral cortex of the brain, rather than abnormalities in the cells of the eye's retina. It is often confused with congenital achromatopsia but underlying physiological deficits of the disorders are completely distinct.

Akinetopsia (Greek: a for "without", kine for "to move" and opsia for "seeing"), also known as cerebral akinetopsia or motion blindness, is a neuropsychological disorder in which a patient cannot perceive motion in their visual field, despite being able to see stationary objects without issue. There are varying degrees of akinetopsia: from seeing motion as a cinema reel to an inability to discriminate any motion. There is currently no effective treatment or cure for akinetopsia.

Inconspicuous akinetopsia is often described by seeing motion as a cinema reel or a multiple exposure photograph. This is the most common kind of akinetopsia and many patients consider the stroboscopic vision as a nuisance. The akinetopsia often occurs with visual trailing (palinopsia), with afterimages being left at each frame of the motion. It is caused by prescription drugs, hallucinogen persisting perception disorder (HPPD), and persistent aura without infarction. The pathophysiology of akinetopsia palinopsia is not known, but it has been hypothesized to be due to inappropriate activation of physiological motion suppression mechanisms which are normally used to maintain visual stability during eye movements (e.g. saccadic suppression).

Vitreomacular adhesion (VMA) is a human medical condition where the vitreous gel (or simply vitreous) of the human eye adheres to the retina in an abnormally strong manner. As the eye ages, it is common for the vitreous to separate from the retina. But if this separation is not complete, i.e. there is still an adhesion, this can create pulling forces on the retina that may result in subsequent loss or distortion of vision. The adhesion in of itself is not dangerous, but the resulting pathological vitreomacular traction (VMT) can cause severe ocular damage.

The current standard of care for treating these adhesions is pars plana vitrectomy (PPV), which involves surgically removing the vitreous from the eye. A biological agent for non-invasive treatment of adhesions called ocriplasmin has been approved by the FDA on Oct 17 2012.

Traction caused by VMA is the underlying pathology of an eye disease called symptomatic VMA. There is evidence that symptomatic VMA can contribute to the development of several well-known eye disorders, such as macular hole and macular pucker, that can cause visual impairment, including blindness. It may also be associated with age-related macular degeneration (AMD), diabetic macular edema (DME), retinal vein occlusion, and diabetic retinopathy (DR).

Reis-Bücklers corneal dystrophy is not associated with any systemic conditions.

The disease has been associated with mutations in TGFBI gene on chromosome 5q which encodes for keratoepithelin. The inheritance is autosomal dominant.

Jalili syndrome is a genetic disorder characterized by the combination of cone-rod dystrophy of the retina and amelogenesis imperfecta. It was characterized in 1988 by Dr. I. K. Jalili and Dr. N. J. D. Smith, following the examination of 29 members of an inbred, Arab family living within the Gaza Strip.

The Jalili syndrome is caused by different mutations all with a linkage at the achromatopsia locus 2q11 on the metal transporter gene, CNNM4. Sequence analysis of this gene within Jalili syndrome sufferers has identified homozygosity or compound heterozygosity for several different mutations in the CNNM4 gene.

Microdeletions in the Y chromosome have been found at a much higher rate in infertile men than in fertile controls and the correlation found may still go up as improved genetic testing techniques for the Y chromosome are developed.

Much study has been focused upon the "azoospermia factor locus" (AZF), at Yq11. A specific partial deletion of AZFc called "gr/gr deletion" is significantly associated with male infertility among Caucasians in Europe and the Western Pacific region.

Additional genes associated with spermatogenesis in men and reduced fertility upon Y chromosome deletions include RBM, DAZ, SPGY, and TSPY.

Iridoplegia is the paralysis of the sphincter of the iris. It can occur in due to direct orbital injury, which may result in short lived blurred vision.

It can be of three types:

1. accommodative iridoplegia- Noncontraction of pupils during accommodation.

2. complete iridoplegia- Iris fails to respond to any stimulation.

3. reflex iridoplegia- The absence of light reflex, with retention of accommodation reflex. Also called Argyll Robertson pupil.