The most common causes of acute bacterial conjunctivitis are "Staphylococcus aureus", "Streptococcus pneumoniae", and "Haemophilus influenzae". Though very rare, hyperacute cases are usually caused by "Neisseria gonorrhoeae" or "N. meningitidis". Chronic cases of bacterial conjunctivitis are those lasting longer than 3 weeks, and are typically caused by "Staphylococcus aureus", "Moraxella lacunata", or gram-negative enteric flora.

Adenoviruses is the most common cause of viral conjunctivitis (adenoviral keratoconjunctivitis). Herpetic keratoconjunctivitis (caused by herpes simplex viruses) can be serious and requires treatment with acyclovir. Acute hemorrhagic conjunctivitis is a highly contagious disease caused by one of two enteroviruses, Enterovirus 70 and Coxsackievirus A24. These were first identified in an outbreak in Ghana in 1969, and have spread worldwide since then, causing several epidemics.

The disease incidence varies widely depending on the geographical location. The most extensive epidemiological survey on this subject has been carried out by Dharmasena et al. who analysed the number of neonates who developed neonatal conjunctivitis in England from 2000 to 2011. In addition to the incidence of this sight threatening infection they also investigated the time trends of the disease. According to them the incidence of Neonatal conjunctivitis (Ophthalmia Neonatorum) in England was 257 (95% confidence interval: 245 to 269) per 100,000 in 2011.

The risk factors associated with BPF are not well known. However, it has been suggested that children under 5 years of age are more susceptible to BPF since they lack serum bactericidal activity against the infection. Older children and adults have much higher titers of bactericidal antibodies, which serve as a protective measure. Also children residing in warmer geographic areas have been associated with a higher risk of BPF infection.

Chemical irritants such as silver nitrate can cause chemical conjunctivitis, usually lasting 2–4 days. Thus, prophylaxis with a 1% silver nitrate solution is no longer in common use. In most countries neomycin and chloramphenicol eye drops are used instead. However, it is possible for newborns to suffer from neonatal conjunctivitis due to reactions with chemicals in these common eye drops. Additionally, a blocked tear duct may be another non-infectious cause of neonatal conjunctivitis.

"Other infections include:"

- "Closed-space infections of the fingertips, known as paronychia."

Several aetiologies are suggested, and any combination of these may be present in any given case.

- Vitamin deficiency (A, B or C)

- Viral infection

- Bacterial infection

- "Leptospira

- "Streptococcus

- "Brucella

- Parasitic infection

- Strongyle

- "Onchocerca cervicalis"

- Autoimmune disease

The disease has been suggested to be primarily autoimmune in nature, being a delayed hypersensitivity reaction to any of the above agents.

One way to prevent allergic rhinitis is to wear a respirator or mask when near potential allergens.

Growing up on a farm and having multiple brothers and or sisters decreases the risk.

The main coagulase-positive staphylococcus is Staphylococcus aureus, although not all strains of Staphylococcus aureus are coagulase positive. These bacteria can survive on dry surfaces, increasing the chance of transmission. S. aureus is also implicated in toxic shock syndrome; during the 1980s some tampons allowed the rapid growth of S. aureus, which released toxins that were absorbed into the bloodstream. Any S. aureus infection can cause the staphylococcal scalded skin syndrome, a cutaneous reaction to exotoxin absorbed into the bloodstream. It can also cause a type of septicaemia called pyaemia. The infection can be life-threatening. Problematically, Methicillin-resistant Staphylococcus aureus (MRSA) has become a major cause of hospital-acquired infections, and is being, MRSA has also been recognized with increasing frequency in community-acquired infections. The symptoms of a Staph Infection include a collection of pus, such as a boil or furuncle, or abscess. The area is typically tender or painful and may be reddened or swollen.

The Appaloosa has a higher risk of developing ERU than other breeds; this predisposition has a genetic basis. Appaloosas which develop ERU are more likely than other breeds to have ERU in both eyes, and more likely to become blind in one or both eyes.

Keratoconjunctivitis is inflammation ("-itis") of the cornea and conjunctiva.

When only the cornea is inflamed, it is called "keratitis"; when only the conjunctiva is inflamed, it is called "conjunctivitis".

There are several potential causes of the inflammation:

- Keratoconjunctivitis sicca is used when the inflammation is due to dryness. ("Sicca" means "dryness" in medical contexts.) It occurs with 20% of rheumatoid arthritis patients.

- The term "Vernal keratoconjunctivitis" (VKC) is used to refer to keratoconjunctivitis occurring in spring, and is usually considered to be due to allergens.

- "Atopic keratoconjunctivitis" is one manifestation of atopy.

- "Epidemic keratoconjunctivitis" is caused by an adenovirus infection.

- "Infectious bovine keratoconjunctivitis" (IBK) is a disease affecting cattle caused by the bacteria "Moraxella bovis".

- "Pink eye in sheep and goat" is another infectious keratoconjunctivitis of veterinary concern, mostly caused by "Chlamydophila pecorum"

- "Superior limbic keratoconjunctivitis" is thought to be caused by mechanical trauma.

- "Keratoconjunctivitis photoelectrica" (arc eye) means inflammation caused by photoelectric UV light. It is a type of ultraviolet keratitis. Such UV exposure can be caused by arc welding without wearing protective eye glass, or by high altitude exposure from sunlight reflected from snow ("snow blindness"). The inflammation will only appear after about 6 to 12 hours. It can be treated by rest, as the inflammation usually heals after 24–48 hours. Proper eye protection should be worn to prevent keratoconjunctivitis photoelectrica.

A study conducted in November of 2017, conveyed a correlation between blepharitis and early onset metabolic syndrome (MetS). To investigate the relationship between blepharitis and MetS, researchers used the Longitudinal Health Insurance Database in Taiwan. Results indicated that hyperlipidaemia and coronary artery disease were significantly correlated with the prior development of blepharitis. Therefore, blepharitis was shown to be significantly related to MetS and can serve as an early indication of the condition.

In another recent study, the presence of Demodex has been unveiled as a common cause of blepharitis. However, the pathogenesis of demodicosis is still unclear. In this study, researchers provide a diagnosis of the disease and propose diagnostic criteria of Demodex blepharitis.

It is usually caused by a form of streptococci viridans bacteria that normally live in the mouth ("Streptococcus mutans, mitis, sanguis "or "milleri").

Other strains of streptococci can also cause subacute endocarditis, streptococcus intermedius:

acute and subacute infection ( can causes about 15% of cases pertaining to infective endocarditis). Additional enterococci (urinary tract infections) and coagulase negative staphylococci can also be causative agents.

The cause of allergic conjunctivitis is an allergic reaction of the body's immune system to an allergen. Allergic conjunctivitis is common in people who have other signs of allergic disease such as hay fever, asthma and eczema.

Among the most common allergens that cause conjunctivitis are:

- Pollen from trees, grass and ragweed

- Animal skin and secretions such as saliva

- Perfumes

- Cosmetics

- Skin medicines

- Air pollution

- Smoke

- Dust mites

- Balsam of Peru (used in food and drink for flavoring, in perfumes and toiletries for fragrance, and in medicine and pharmaceutical items for healing properties)

- Eye drops

Most cases of seasonal conjunctivitis are due to pollen and occur in the hay fever season, grass pollens in early summer and various other pollens and moulds may cause symptoms later in the summer.

Allergic rhinitis triggered by the pollens of specific seasonal plants is commonly known as "hay fever", because it is most prevalent during haying season. However, it is possible to have allergic rhinitis throughout the year. The pollen that causes hay fever varies between individuals and from region to region; in general, the tiny, hardly visible pollens of wind-pollinated plants are the predominant cause. Pollens of insect-pollinated plants are too large to remain airborne and pose no risk. Examples of plants commonly responsible for hay fever include:

- Trees: such as pine ("Pinus"), birch ("Betula"), alder ("Alnus"), cedar ("Cedrus"), hazel ("Corylus"), hornbeam ("Carpinus"), horse chestnut ("Aesculus"), willow ("Salix"), poplar ("Populus"), plane ("Platanus"), linden/lime ("Tilia"), and olive ("Olea"). In northern latitudes, birch is considered to be the most common allergenic tree pollen, with an estimated 15–20% of people with hay fever sensitive to birch pollen grains. A major antigen in these is a protein called Bet V I. Olive pollen is most predominant in Mediterranean regions. Hay fever in Japan is caused primarily by sugi ("Cryptomeria japonica") and hinoki ("Chamaecyparis obtusa") tree pollen.

- "Allergy friendly" trees include: ash (female only), red maple, yellow poplar, dogwood, magnolia, double-flowered cherry, fir, spruce, and flowering plum.

- Grasses (Family Poaceae): especially ryegrass ("Lolium" sp.) and timothy ("Phleum pratense"). An estimated 90% of people with hay fever are allergic to grass pollen.

- Weeds: ragweed ("Ambrosia"), plantain ("Plantago"), nettle/parietaria (Urticaceae), mugwort ("Artemisia Vulgaris"), Fat hen ("Chenopodium"), and sorrel/dock ("Rumex")

Allergic rhinitis may also be caused by allergy to Balsam of Peru, which is in various fragrances and other products.

The mechanism of subacute bacterial endocarditis could be due to malformed stenotic valves which in the company of bacteremia, become infected, via adhesion and subsequent colonization of the surface area. This causes an inflammatory response, with recruitment of matrix metalloproteinases, and destruction of collagen.

Underlying structural valve disease is usually present in patients before developing subacute endocarditis, and is less likely to lead to septic emboli than is acute endocarditis, but subacute endocarditis has a relatively slow process of infection and, if left untreated, can worsen for up to one year before it is fatal. In cases of subacute bacterial endocarditis, the causative organism (streptococcus viridans) needs a previous heart valve disease to colonize. On the other hand, in cases of acute bacterial endocarditis, the organism can colonize on the healthy heart valve, causing the disease.

The mechanism by which the bacteria causes symptoms of blepharitis is not fully understood and may include direct irritation of bacterial toxins and/or enhanced cell-mediated immunity to S. aureus.

Staphylococcal blepharitis is caused by an infection of the anterior portion of the eyelid by Staphylococcal bacteria. In a study of ocular flora, 46% to 51% of those diagnosed with staphylococcal blepharitis had cultures positive for Staphylococcus aureus in comparison to 8% of normal patients. Staphylococcal blepharitis may start in childhood and continue into adulthood. It is commonly recurrent and it requires special medical care. The prevalence of Staphylococcus aureus in the conjunctival sac and on the lid margin varies among countries, likely due to differences in climate and environment. Seborrheic blepharitis is characterized by less inflammation than Staphylococcal blepharitis; however, it causes more excess oil or greasy scaling. Meibomian Gland Dysfunction is a result of abnormalities of the meibomian glands and altered secretion meibum, which plays an imperative role in lagging the evaporation of tear films and smoothing of the tear film to produce an even optical surface. Posterior blepharitis is an inflammation of the eyelids, secondary to dysfunction of the meibomian glands. Like anterior blepharitis, it is a bilateral chronic condition and may be associated with skin rosacea. There is growing evidence that, in some cases, it is caused by Demodex mites.

The eye gnat ("Liohippelates") was thought to be the cause of the conjunctivitis epidemic which occurred in Mato Grosso do Sul in 1991. These gnats were extracted from the conjunctival secretions of the children who were infected with conjunctivitis. 19 of those children developed BPF following the conjunctivitis. Other modes of transmission include contact with the conjunctival discharges of infected people, ophthalmic instruments which have not been properly sterilized, sharing eye makeup applicators or multiple-dose eye medications.

Ultraviolet (UV) radiation is implicated in cattle with no pigmentation around the eyelids and cattle with prominently placed eyes. Exudate from the sun-burnt skin around the eyes can contain bacteria and attracts flies. UV light also directly damages the corneal epithelium, leading to a breakdown in host innate immunity.

Dust, dried-up plants, tall vegetation, and oversized or incorrectly placed ear tags may cause mechanical damage to the eye and facilitate bacterial colonization.

The disease may be complicated by concurrent infection with viruses such as infectious bovine rhinotracheitis virus (bovine herpesvirus 1) or adenovirus, bacteria such as "Mycoplasma boviculi" or "Listeria monocytogenes", or infestation by "Thelazia", a nematode.

Vitamin A deficiency is also implicated.

IBK is most prevalent in summer and early autumn.

A recent Meat and Livestock Australia report "estimates that the disease costs Australian beef producers AU$23.5 million annually in lost production and treatment costs".

PKC results from a delayed hypersensitivity/inflammatory reaction to antigens expressed by various pathogens. Common agents include Staph. aureus, Mycobacterium tuberculosis, Chlamydia and Candida.

It is usually caused by allergies or viral infections, often inciting excessive eye rubbing. Chemosis is also included in the Chandler Classification system of orbital infections.

If chemosis has occurred due to excessive rubbing of the eye, the first aid to be given is a cold water wash for eyes.

Other causes of chemosis include:

- Superior vena cava obstruction, accompanied by facial oedema

- Hyperthyroidism, associated with exophthalmos, periorbital puffiness, lid retraction, and lid lag

- Cavernous sinus thrombosis, associated with infection of the paranasal sinuses, proptosis, periorbital oedema, retinal haemorrhages, papilledema, extraocular movement abnormalities, and trigeminal nerve sensory loss

- Carotid-cavernous fistula - classic triad of chemosis, pulsatile proptosis, and ocular bruit

- Cluster headache

- Trichinellosis

- Systemic lupus erythematosus (SLE)

- Angioedema

- Acute glaucoma

- Panophthalmitis

- Orbital cellulitis

- Gonorrheal conjunctivitis

- Dacryocystitis

- Spitting cobra venom to the eye

- High concentrations of phenacyl chloride in chemical mace spray

- Urticaria

- Trauma

- Post surgical

- Rhabdomyosarcoma of the orbit

There is low or very-low quality evidence that probiotics may be better than placebo in preventing acute URTIs. Vaccination against influenza viruses, adenoviruses, measles, rubella, "Streptococcus pneumoniae", "Haemophilus influenzae", diphtheria, "Bacillus anthracis", and "Bordetella pertussis" may prevent them from infecting the URT or reduce the severity of the infection.

"Moraxella bovis" is a Gram-negative rod-shaped aerobe. This bacterium is an obligate intracellular parasite of the mucous membranes, and can usually be isolated from the respiratory tract, vagina, and conjunctiva of healthy animals. Transmission of IBK is through direct contact with mucous membranes and their secretions and indirect contact where flies act as a mechanical vector. Asymptomatic carrier animals can also be source of infection.

Most household disinfectants will inactivate FHV-1. The virus can survive up to 18 hours in a damp environment, but less in a dry environment and only shortly as an aerosol.

FVR is transmitted through direct contact only. It replicates in the nasal and nasopharyngeal tissues and the tonsils. Viremia (the presence of the virus in the blood) is rare. The virus is shed in saliva and eye and nasal secretions, and can also be spread by fomites. FVR has a two- to five-day incubation period. The virus is shed for one to three weeks postinfection. Latently infected cats (carriers) will shed FHV-1 intermittently for life, with the virus persisting within the trigeminal ganglion. Stress and use of corticosteroids precipitate shedding. Most disinfectants, antiseptics and detergents are effective against the virus.