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%.

Dichromacy ("di" meaning "two" and "chroma" meaning "color") is the state of having two types of functioning color receptors, called cone cells, in the eyes. Organisms with dichromacy are called dichromats. Dichromats can match any color they see with a mixture of no more than two pure spectral lights. By comparison, trichromats require three pure spectral lights to match all colors that they can perceive, and tetrachromats require four.

Dichromacy in humans is a color vision defect in which one of the three basic color mechanisms is absent or not functioning. It is hereditary and sex-linked, predominantly affecting males. Dichromacy occurs when one of the cone pigments is missing and color is reduced to two dimensions.

There are various kinds of color blindness:

- Protanopia is a severe form of red-green color blindness, in which there is impairment in perception of very long wavelengths, such as reds. To these individuals, reds are perceived as beige or grey and greens tend to look beige or grey like reds. It is also the most common type of dichromacy today. This problem occurs because patients do not have the red cone cells in the retina. Protanomaly is a less severe version.

- Deuteranopia consists of an impairment in perceiving medium wavelengths, such as greens. Deuteranomaly is a less severe form of deuteranopia. Those with deuteranomaly cannot see reds and greens like those without this condition; however, they can still distinguish them in most cases. It is very similar to protanopia. In this form, patients do not have green cone cells in the retina, which makes it hard to see the green color.

- A rarer form of color blindness is tritanopia, where there exists an inability to perceive short wavelengths, such as blues. Sufferers have trouble distinguishing between yellow and blue. They tend to confuse greens and blues, and yellow can appear pink. This is the rarest of all dichromacy, and occurs in around 1 in 100,000 people. Patients do not have the blue cone cells in the retina.

Heterochromia has also been observed in those with Duane syndrome.

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.

The odd-eyed coloring is caused when either the epistatic (dominant) white gene (which masks any other color genes and turns a cat completely white) or the white spotting gene (which is the gene responsible for bicolor and tuxedo cats) prevents melanin (pigment) granules from reaching one eye during development, resulting in a cat with one blue eye and one green, yellow, or brown eye. The condition only rarely occurs in cats that lack both the dominant white and the white spotting gene.

An odd-eyed cat is a cat with one blue eye and one eye either green, yellow, or brown. This is a feline form of complete heterochromia, a condition that occurs in some other animals. The condition most commonly affects white-colored cats, but may be found in a cat of any color, provided that it possesses the white spotting gene.

Males and Females get Mongolian spots equally. A hospital-based, cross-sectional, prospective study was conducted in the Department of Dermatology, Venereology and Leprosy, BLDE University, Shri B. M. Patil Medical College Hospital and Research Center, Bijapur. One thousand neonates delivered in the Department of Obstetrics and Gynecology of the same institution was surveyed for the presence of skin lesions. The study was conducted in the period of November 2007 to May 2009. The study showed that 467 males were born with Mongolian spots and 380 females were born with Mongolian spots. The results showed there was no statistical significance in males and females born with Mongolian spots. Within the same study, different racial groups were recorded and documented. The study showed that among the Australian neonate, 25.5% were born with Mongolian spots. In the Iranian neonate, 71-81% were reported, in the Japanese neonate 81.5%, in the Turkish neonate 13.2%, in the caucasian neonate 62.8%, in the African American neonate 86.6%, and in the Indian neonate 72-89% were reported in having Mongolian spots. The populations with the most incidences of Mongolian spots were Iranian, Japanese, African American, and Indian.

Achromatopsia (ACHM), also known as total color blindness, is a medical syndrome that exhibits symptoms relating to at least five conditions. The term may refer to acquired conditions such as cerebral achromatopsia, also known as color agnosia, but it typically refers to an autosomal recessive congenital color vision condition, the inability to perceive color and to achieve satisfactory visual acuity at high light levels (typically exterior daylight). The syndrome is also present in an incomplete form which is more properly defined as dyschromatopsia. It is estimated to affect 1 in 40,000 live births worldwide.

There is some discussion as to whether achromats can see color or not. As illustrated in "The Island of the Colorblind" by Oliver Sacks, some achromats cannot see color, only black, white, and shades of grey. With five different genes currently known to cause similar symptoms, it may be that some do see marginal levels of color differentiation due to different gene characteristics. With such small sample sizes and low response rates, it is difficult to accurately diagnose the 'typical achromatic conditions'. If the light level during testing is optimized for them, they may achieve corrected visual acuity of 20/100 to 20/150 at lower light levels, regardless of the absence of color. One common trait is hemeralopia or blindness in full sun. In patients with achromatopsia, the cone system and fibres carrying color information remain intact. This indicates that the mechanism used to construct colors is defective.

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.

Mongolian spots, or Dermal melanocytosis, result from failure of complete melanocyte migration into the epidermis before birth with ensuing dermal nesting and melanin production. If there are many spots, or a spot covers a large area, it may be a sign of an underlying disorder, such as a metabolism problem called GM1 gangliosidosis Type 1. Recent data suggest that Mongolian spots may be associated with inborn errors of metabolism. Inborn errors of metabolism arise from single gene defect, most often involving an enzyme function, which leads to disruption of a specific metabolic pathway giving rise to abnormalities in the synthesis or catabolism or proteins, fats or carbohydrates. The most common condition associated with Mongolian spots is Hurler's disease followed by GM1 gangliosidosis Type 1. The clinical manifestations in Mongolian spots in inborn errors of metabolism are spots deeper in color and have a generalized distribution involving dorsal and ventral trunk in addition to sacral region and extremities. They are persistent and in some cases an indistinct feathery border has been described. Another possible cause is through genetic inheritance. Mongolian spots have been diagnosed on several occasions through family history, Mongolian spots were linked with an autosomal dominant inheritance. The majority of the neonatal cutaneous lesions are physiological and transient requiring no therapy. It is necessary to differentiate between benign and clinically significant skin lesions in newborn. Therefore, it is important to be aware of the innocent transient skin lesions in newborn and differentiate these from other serious conditions, which will help avoid unnecessary therapy to the neonates. Parents can be assured of good prognosis of these skin manifestations.

Synesthesia is found in at least 4.4% of the population, as a high estimate, which is equivalent to 1 in 23 people. This study had also concluded that one common form of synesthesia—grapheme-color synesthesia (colored letters and numbers) – is found in more than one percent of the population, and this latter prevalence of graphemes-color synesthesia has now been independently verified in a yet larger sample. Earlier estimates of the prevalence of synesthesia were based on "best-guess" estimations only ("e.g." 1 in 250,000) or had limitations in their methodologies because they required synesthetes to refer themselves for study ("e.g." 1 in 2000) and for this reason the authors of those studies had been moderate in their claims. Also, some individuals will not self-classify as synesthetes because they do not realize that their perceptions are different from those of everyone else.

The most common forms of synesthesia are those that trigger colors, and the most prevalent of all is day-color. Also relatively common is grapheme-color synesthesia. We can think of "prevalence" both in terms of how common is synesthesia (or different forms of synesthesia) within the population, or how common are different forms of synesthesia within synesthetes. So within synesthetes, forms of synesthesia that trigger color also appear to be the most common forms of synesthesia with a prevalence rate of 86% within synesthetes. In another study, music-color is also prevalent at 18–41%. Some of the rarest are reported to be auditory-tactile, mirror-touch, and lexical-gustatory.

There is research to suggest that the likelihood of having synesthesia is greater in people with autism.

Nyctalopia (from Greek νύκτ-, "nykt-" "night"; ἀλαός, "alaos" "blind, not seeing", and ὄψ, "ops" "eye"), also called night-blindness, is a condition making it difficult or impossible to see in relatively low light. It is a symptom of several eye diseases. Night blindness may exist from birth, or be caused by injury or malnutrition (for example, vitamin A deficiency). It can be described as insufficient adaptation to darkness.

The most common cause of nyctalopia is retinitis pigmentosa, a disorder in which the rod cells in the retina gradually lose their ability to respond to the light. Patients suffering from this genetic condition have progressive nyctalopia and eventually their daytime vision may also be affected. In X-linked congenital stationary night blindness, from birth the rods either do not work at all, or work very little, but the condition doesn't get worse.

Another cause of night blindness is a deficiency of retinol, or vitamin A, found in fish oils, liver and dairy products.

The opposite problem, the inability to see in bright light, is known as "hemeralopia" and is much rarer.

Since the outer area of the retina is made up of more rods than cones, loss of peripheral vision often results in night blindness. Individuals suffering from night blindness not only see poorly at night, but also require extra time for their eyes to adjust from brightly lit areas to dim ones. Contrast vision may also be greatly reduced.

Rods contain a receptor-protein called rhodopsin. When light falls on rhodopsin, it undergoes a series of conformational changes ultimately generating electrical signals which are carried to the brain via the optic nerve. In the absence of light, rhodopsin is regenerated. The body synthesizes rhodopsin from vitamin A, which is why a deficiency in vitamin A causes poor night vision.

Refractive "vision correction" surgery (especially PRK with the complication of "haze") may rarely cause a reduction in best night-time acuity due to the impairment of contrast sensitivity function (CSF) which is induced by intraocular light-scatter resulting from surgical intervention in the natural structural integrity of the cornea.

Lethal white syndrome (LWS), also called overo lethal white syndrome (OLWS), lethal white overo (LWO), and overo lethal white foal syndrome (OLWFS), is an autosomal genetic disorder most prevalent in the American Paint Horse. Affected foals are born after the full 11-month gestation and externally appear normal, though they have all-white or nearly all-white coats and blue eyes. However, internally, these foals have a nonfunctioning colon. Within a few hours, signs of colic appear; affected foals die within a few days. Because the death is often painful, such foals often are humanely euthanized once identified. The disease is particularly devastating because foals are born seemingly healthy after being carried to full term.

The disease has a similar cause to Hirschsprung's disease in humans. A mutation in the middle of the endothelin receptor type B (EDNRB) gene causes lethal white syndrome when homozygous. Carriers, which are heterozygous—that is, have one copy of the mutated allele, but themselves are healthy—can now be reliably identified with a DNA test. Both parents must be carriers of one copy of the LWS allele for an affected foal to be born.

Horses that are heterozygous for the gene that causes lethal white syndrome often exhibit a spotted coat color pattern commonly known as "frame" or "frame overo". Coat color alone does not always indicate the presence of LWS or carrier status, however. The frame pattern may be minimally expressed or masked by other spotting patterns. Also, different genetic mechanisms produce healthy white foals and have no connection to LWS, another reason for genetic testing of potential breeding stock. Some confusion also occurs because the term overo is used to describe a number of other non tobiano spotting patterns besides the frame pattern. Though no treatment or cure for LWS foals is known, a white foal without LWS that appears ill may have a treatable condition.

Congenital stationary night blindness is also an ophthalmologic disorder in horses with leopard spotting patterns, such as the Appaloosa. It is present at birth (congenital), not sex-linked, non-progressive and affects the animal's vision in conditions of low lighting. CSNB is usually diagnosed based on the owner's observations, but some horses have visibly abnormal eyes: poorly aligned eyes (dorsomedial strabismus) or involuntary eye movement (nystagmus). In horses, CSNB has been linked with the leopard complex color pattern since the 1970s. A 2008 study theorizes that both CSNB and leopard complex spotting patterns are linked to the TRPM1 gene. The region on horse chromosome 1 to which the "Lp" gene has now been localized also encodes a protein that channels calcium ions, a key factor in the transmission of nerve impulses. This protein, found in the retina and the skin, exists in fractional percentages of the normal levels found in homozygous "Lp/Lp" horses and so compromises the basic chemical reaction for nerve impulse transmission.

The genetic mechanism of synesthesia has long been debated. Due to the prevalence of synesthesia among the first-degree relatives of synesthetes, there is evidence that synesthesia might have a genetic basis, however the monozygotic twins case studies indicate there is an epigenetic component. Synesthesia might also be a oligogenic condition, with Locus heterogeneity, multiple forms of inheritance (including Mendelian in some cases), and continuous variation in gene expression.

Not all white, blue-eyed foals are affected with LWS. Other genes can produce healthy pink-skinned, blue-eyed horses with a white or very light cream-colored coat. For a time, some of these completely white horses were called "living lethals", but this is a misnomer. Before reliable information and the DNA test were available to breeders, perfectly healthy, white-coated, blue-eyed foals were sometimes euthanized for fear they were lethal whites, an outcome which can be avoided today with testing and a better understanding of coat color genetics or even waiting 12 hours or so for the foal to develop clinical signs. The availability of testing also allows a breeder to determine if a white-coated, blue-eyed foal that becomes ill is an LWS foal that requires euthanasia or a non-LWS foal with a simple illness that may be successfully treated.

- Double-cream dilutes such as cremello, perlinos, and smoky creams, have cream-colored coats, blue eyes, and pink skin. The faint cream pigmentation of their coats can be distinguished from the unpigmented white markings and underlying unpigmented pink skin. A similar-looking "pseudo double dilute" can be produced with help from the pearl gene or "barlink factor" or the champagne gene.

- The combination of tobiano with other white spotting patterns can produce white or nearly white horses, which may have blue eyes.

- Sabino horses that are homozygous for the sabino-1 ("Sb-1") gene are often called "sabino-white", and are all- or nearly all-white. Not all sabino horses carry "Sb-1".

- Dominant white genetics are not thoroughly understood, but are characterized by all- or nearly all-white coats.

"Seeing pink elephants" is a euphemism for drunken hallucination caused by alcoholic hallucinosis or delirium tremens. The term dates back to at least the early 20th century, emerging from earlier idioms about snakes and other creatures. An alcoholic character in Jack London's 1913 novel "John Barleycorn" is said to hallucinate "blue mice and pink elephants".

Closed-eye hallucinations and closed-eye visualizations (CEV) are a distinct class of hallucination. These types of hallucinations generally only occur when one's eyes are closed or when one is in a darkened room. They can be a form of phosphene. Some people report closed-eye hallucinations under the influence of psychedelics. These are reportedly of a different nature than the "open-eye" hallucinations of the same compounds.

The lack of nutrients in the diet, or the lack of a balanced diet, can contribute to the discoloration of the area under the eyes. It is believed that iron deficiency can cause dark circles as well. Iron deficiency is the most common type of anemia and this condition is a sign that not enough oxygen is getting to the body tissues.

The skin can also become more pale during pregnancy and menstruation (due to lack of iron), allowing the underlying veins under the eyes to become more visible.

Lavender foal syndrome is thought to be created by an autosomal recessive gene. When a horse is heterozygous for the gene, it is a carrier, but healthy and has no clinical signs of the condition. If two carriers are bred together, however, classic Mendelian genetics indicate a 25% chance of any given mating producing a homozygous foal, hence affected by the disease. Carrier horses can be bred and produce non-affected foals, as long as they are bred with a non-carrier for the LFS gene. It is hypothesized, though untested, that LFS may be linked to another genetic disease that affects Egyptian-related Arabians, juvenile epilepsy. This theory has been raised because of a small number of horses that have produced both LFS and epileptic foals.

LFS is one of six genetic diseases known to affect horses of Arabian bloodlines. Genetic diseases affect other horse breeds, including different coat color-based lethals, such as lethal white syndrome. In addition, the color white in horses, when created by certain alleles of "dominant white" (W), may possibly be fatal if homozygous.

Ultraviolet light from the sun causes premature aging of the skin and skin damage that can lead to melanoma. Some scientists hypothesize that overexposure to UV, including excessive sunlight, may play a role in the formation of acquired moles. However, more research is needed to determine the complex interaction between genetic makeup and overall exposure to ultraviolet light. Some strong indications that this is so (but falling short of proof), are:

- The relative lack of moles on the buttocks of people with dysplastic nevi.

- Freckles (spots of melanin on the skin, and distinct from moles) are known to be influenced by sunlight.

Studies have found that sunburns and too much time in the sun can increase the risk factors for melanoma. This is "in addition to" those who have dysplastic nevi being at higher risk of this cancer (the uncertainty is in regard to acquiring "benign" moles). To prevent and reduce the risk of melanoma caused by UV radiation, the American Academy of Dermatology and the National Cancer Institute recommends staying out of the sun between 10 a.m. and 4 p.m. standard time (or whenever one's shadow is shorter than one's height). The National Cancer Institute also recommends wearing long sleeves and trousers, hats with a wide brim, sunscreens, and sunglasses that have UV-deflecting lenses.

Controversies exist around eliminating this disorder from breeding Collies. Some veterinarians advocate only breeding dogs with no evidence of disease, but this would eliminate a large portion of potential breeding stock. Because of this, others recommend only breeding mildly affected dogs, but this would never completely eradicate the condition. Also, mild cases of choroidal hypoplasia may become pigmented and therefore undiagnosable by the age of three to seven months. If puppies are not checked for CEA before this happens, they may be mistaken for normal and bred as such. Checking for CEA by seven weeks of age can eliminate this possibility. Diagnosis is also difficult in dogs with coats of dilute color because lack of pigment in the choroid of these animals can be confused with choroidal hypoplasia. Also, because of the lack of choroidal pigment, mild choroidal hypoplasia is difficult to see, and therefore cases of CEA may be missed.

Until recently, the only way to know if a dog was a carrier was for it to produce an affected puppy. However, a genetic test for CEA became available at the beginning of 2005, developed by the Baker Institute for Animal Health, Cornell University, and administered through OptiGen. The test can determine whether a dog is affected, a carrier, or clear, and is therefore a useful tool in determining a particular dog's suitability for breeding.

There are five known levels of CEV perception which can be achieved either through chemical stimuli or through meditative relaxation techniques. Level 1 and 2 are very common and often happen every day. It is still normal to experience level 3, and even level 4, but only a small percentage of the population does this without psychedelic drugs, meditation or extensive visualization training.