Viruses are common causes of the common cold. Less often, bacteria may also cause pharyngitis. Both of these organisms enter the body via the nose or mouth as aerosolized particles when someone sneezes or coughs. Because many germs are contagious, one can even acquire them from touching utensils, toys, personal care products or door knobs. The most common viruses that causes throat irritation include the common cold virus, influenza, infectious mononucleosis, measles and croup. Most bacteria and viruses usually induce throat irritation during the winter or autumn.

When the environment is dry especially in winter, it can create a sensation of dryness and a scratchy feeling in the throat. This is most commonly observed in the morning. Other individuals who also develop throat irritation are those breathing through their mouth because of a congested nose.

Environmental pollution is also a common cause of throat irritation. In fact, indoor pollution because of tobacco smoke used to be a common cause of throat irritation. Other items known to induce throat irritation include alcohol, spicy or hot foods and smokeless tobacco.

Rhinorrhea can also occur when individuals with allergies to certain substances, such as pollen, dust, latex, soy, shellfish, or animal dander, are exposed to these allergens. In people with sensitized immune systems, the inhalation of one of these substances triggers the production of the antibody immunoglobulin E (IgE), which binds to mast cells and basophils. IgE bound to mast cells are stimulated by pollen and dust, causing the release of inflammatory mediators such as histamine. In turn, this causes, among other things, inflammation and swelling of the tissue of the nasal cavities as well as increased mucus production. Particulate matter in polluted air and chemicals such as chlorine and detergents, which can normally be tolerated, can make the condition considerably worse.

Rhinorrhea can be a symptom of other diseases, such as the common cold or influenza. During these infections, the nasal mucous membranes produce excess mucus, filling the nasal cavities. This is to prevent infection from spreading to the lungs and respiratory tract, where it could cause far worse damage. It has also been suggested that rhinorrhea is a result of viral evolution, and may be a response that is not useful to the host, but which has evolved by the virus to maximise its own infectivity. Rhinorrhea caused by these infections usually occur on circadian rhythms. Over the course of a viral infection, sinusitis (the inflammation of the nasal tissue) may occur, causing the mucous membranes to release more mucus. Acute sinusitis consists of the nasal passages swelling during a viral infection. Chronic sinusitis occurs when one or more nasal polyps appear. This can be caused by a deviated septum as well as a viral infection.

Laryngitis that continues for more than three weeks is considered chronic. If laryngeal symptoms last for more than three weeks, a referral should be made for further examination, including direct laryngoscopy. The prognosis for chronic laryngitis varies depending on the cause of the laryngitis.

Pharyngitis may also be caused by mechanical, chemical or thermal irritation, for example cold air or acid reflux. Some medications may produce pharyngitis such as pramipexole and antipsychotics.

Some cases of pharyngitis are caused by fungal infection such as Candida albicans causing oral thrush.

The traditional theory is that a cold can be "caught" by prolonged exposure to cold weather such as rain or winter conditions, which is how the disease got its name. Some of the viruses that cause the common colds are seasonal, occurring more frequently during cold or wet weather. The reason for the seasonality has not been conclusively determined. Possible explanations may include cold temperature-induced changes in the respiratory system, decreased immune response, and low humidity causing an increase in viral transmission rates, perhaps due to dry air allowing small viral droplets to disperse farther and stay in the air longer.

The apparent seasonality may also be due to social factors, such as people spending more time indoors, near infected people, and specifically children at school. There is some controversy over the role of low body temperature as a risk factor for the common cold; the majority of the evidence suggests that it may result in greater susceptibility to infection.

The common cold virus is typically transmitted via airborne droplets (aerosols), direct contact with infected nasal secretions, or fomites (contaminated objects). Which of these routes is of primary importance has not been determined; however, hand-to-hand and hand-to-surface-to-hand contact seems of more importance than transmission via aerosols. The viruses may survive for prolonged periods in the environment (over 18 hours for rhinoviruses) and can be picked up by people's hands and subsequently carried to their eyes or nose where infection occurs. Transmission is common in daycare and at school due to the proximity of many children with little immunity and frequently poor hygiene. These infections are then brought home to other members of the family. There is no evidence that recirculated air during commercial flight is a method of transmission. People sitting in close proximity appear to be at greater risk of infection.

Rhinovirus-caused colds are most infectious during the first three days of symptoms; they are much less infectious afterwards.

Children have 2-9 viral respiratory illnesses per year. In 2013 18.8 billion cases of upper respiratory infections were reported. As of 2014, upper respiratory infections caused about 3,000 deaths down from 4,000 in 1990. In the United States, URIs are the most common infectious illness in the general population. URIs are the leading reasons for people missing work and school.

Acute laryngitis may persist, but will typically resolve on its own within two weeks. Recovery is likely to be quick if the patient follows the treatment plan. In viral laryngitis, symptoms can persist for an extended amount of time, even when upper respiratory tract inflammation has been resolved.

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.

Across all posited aetiologies, contact granulomas are more commonly observed in male patients than in female patients, and more commonly in adult patients than in pediatric patients. In cases where gastroesophageal reflux disease is identified as the most likely cause of the granuloma, the patient is most commonly an adult man in his 30s or 40s. When contact granulomas do occur in female and pediatric patients, they usually occur post-intubation. There are no observable age or gender trends within the category of post-intubation patients suffering from contact granulomas, nor within the causation category of vocal abuse history.

In the case of infectious rhinitis, vaccination against influenza viruses, adenoviruses, measles, rubella, "Streptococcus pneumoniae", "Haemophilus influenzae", diphtheria, "Bacillus anthracis", and "Bordetella pertussis" may help prevent it.

Acute bronchitis is one of the most common diseases. About 5% of adults are affected and about 6% of children have at least one episode a year. It occurs more often in the winter.

In infants under one year of age, acute bronchitis was the most common reason for admission to the hospital after an emergency department visit in the US in 2011.

Nonallergic rhinitis refers to rhinitis that is not due to an allergy. The category was formerly referred to as vasomotor rhinitis, as the first cause discovered was vasodilation due to an overactive parasympathetic nerve response. As additional causes were identified, additional types of nonallergic rhinitis were recognized. Vasomotor rhinitis is now included among these under the more general classification of nonallergic rhinitis. The diagnosis is made upon excluding allergic causes. It is an umbrella term of rhinitis of multiple causes, such as occupational (chemical), smoking, gustatory, hormonal, senile (rhinitis of the elderly), atrophic, medication-induced (including rhinitis medicamentosa), local allergic rhinitis, non-allergic rhinitis with eosinophilia syndrome (NARES) and idiopathic (vasomotor or non-allergic, non-infectious perennial allergic rhinitis (NANIPER), or non-infectious non-allergic rhinitis (NINAR).

In vasomotor rhinitis, certain nonspecific stimuli, including changes in environment (temperature, humidity, barometric pressure, or weather), airborne irritants (odors, fumes), dietary factors (spicy food, alcohol), sexual arousal, exercise, and emotional factors trigger rhinitis. There is still much to be learned about this, but it is thought that these non-allergic triggers cause dilation of the blood vessels in the lining of the nose, which results in swelling and drainage.

Non-allergic rhinitis can co-exist with allergic rhinitis, and is referred to as "mixed rhinitis." The pathology of vasomotor rhinitis appears to involve neurogenic inflammation and is as yet not very well understood. Vasomotor rhinitis appears to be significantly more common in women than men, leading some researchers to believe that hormones play a role. In general, age of onset occurs after 20 years of age, in contrast to allergic rhinitis which can be developed at any age. Individuals with vasomotor rhinitis typically experience symptoms year-round, though symptoms may be exacerbated in the spring and autumn when rapid weather changes are more common. An estimated 17 million United States citizens have vasomotor rhinitis.

Drinking alcohol may cause rhinitis as well as worsen asthma (see alcohol-induced respiratory reactions). In certain populations, particularly those of East Asian countries such as Japan, these reactions have a nonallergic basis. In other populations, particularly those of European descent, a genetic variant in the gene that metabolizes ethanol to acetaldehyde, ADH1B, is associated with alcohol-induced rhinitis. It is suggested that this variant metabolizes ethanol to acetaldehyde too quickly for further processing by ALDH2 and thereby leads to the accumulation of acetaldehyde and rhinitis symptoms. In these cases, alcohol-induced rhinitis may be of the "mixed rhinitis" type and, it seems likely, most cases of alcohol-induced rhinitis in non-Asian populations reflect true allergic response to the non-ethanol and/or contaminants in alcoholic beverages, particularly when these beverages are wines or beers. Alcohol-exacerbated rhinitis is more frequent in individuals with a history of rhinitis exacerbated by aspirin.

Aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs), particularly those that inhibit cyclooxygenase 1 (COX1), can worsen rhinitis and asthma symptoms in individuals with a history of either one of these diseases. These exacerbations most often appear due to NSAID hypersensitivity reactions rather than NSAID-induced allergic reactions.

The antihistamine azelastine, applied as a nasal spray, may be effective for vasomotor rhinitis. Fluticasone propionate or budesonide (both are steroids) in nostril spray form may also be used for symptomatic treatment. The antihistamine cyproheptadine is also effective, probably due to its antiserotonergic effects.

A Cochrane review on non-allergic rhinitis reports improvement of overall function after treatment with capsaicin (the active component of chili peppers). The quality of evidence is low, however.

Acute bronchitis usually lasts a few days or weeks. It may accompany or closely follow a cold or the flu, or may occur on its own. Bronchitis usually begins with a dry cough, including waking the sufferer at night. After a few days, it progresses to a wetter or productive cough, which may be accompanied by fever, fatigue, and headache. The fever, fatigue, and malaise may last only a few days, but the wet cough may last up to several weeks.

Should the cough last longer than a month, some physicians may issue a referral to an otorhinolaryngologist (ear, nose and throat doctor) to see if a condition other than bronchitis is causing the irritation. It is possible that having irritated bronchial tubes for as long as a few months may inspire asthmatic conditions in some patients.

In addition, if one starts coughing mucus tinged with blood, one should see a physician. In rare cases, physicians may conduct tests to see whether the cause of the bloody sputum is a serious condition such as tuberculosis or lung cancer.

Since the advent of penicillin in the 1940s, a major preoccupation in the treatment of streptococcal tonsillitis has been the prevention of rheumatic fever, and its major effects on the nervous system (Sydenham's chorea) and heart. Recent evidence would suggest that the rheumatogenic strains of group A beta hemolytic strep have become markedly less prevalent and are now only present in small pockets such as in Salt Lake City, USA. This brings into question the rationale for treating tonsillitis as a means of preventing rheumatic fever.

Complications may rarely include dehydration and kidney failure due to difficulty swallowing, blocked airways due to inflammation, and pharyngitis due to the spread of infection.

An abscess may develop lateral to the tonsil during an infection, typically several days after the onset of tonsillitis. This is termed a peritonsillar abscess (or quinsy).

Rarely, the infection may spread beyond the tonsil resulting in inflammation and infection of the internal jugular vein giving rise to a spreading septicaemia infection (Lemierre's syndrome).

In chronic/recurrent cases (generally defined as seven episodes of tonsillitis in the preceding year, five episodes in each of the preceding two years or three episodes in each of the preceding three years), or in acute cases where the palatine tonsils become so swollen that swallowing is impaired, a tonsillectomy can be performed to remove the tonsils. Patients whose tonsils have been removed are still protected from infection by the rest of their immune system.

In strep throat, very rarely diseases like rheumatic fever or glomerulonephritis can occur. These complications are extremely rare in developed nations but remain a significant problem in poorer nations. Tonsillitis associated with strep throat, if untreated, is hypothesized to lead to pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections (PANDAS).

The symptoms of strep throat usually improve within three to five days, irrespective of treatment. Treatment with antibiotics reduces the risk of complications and transmission; children may return to school 24 hours after antibiotics are administered. The risk of complications in adults is low. In children, acute rheumatic fever is rare in most of the developed world. It is, however, the leading cause of acquired heart disease in India, sub-Saharan Africa and some parts of Australia.

Complications arising from streptococcal throat infections include:

- Acute rheumatic fever

- Scarlet fever

- Streptococcal toxic shock syndrome

- Glomerulonephritis

- PANDAS syndrome

- Peritonsillar abscess

- Cervical lymphadenitis

- Mastoiditis

The economic cost of the disease in the United States in children is approximately $350 million annually.

The most common cause is viral infection and includes adenovirus, rhinovirus, influenza, coronavirus, and respiratory syncytial virus. It can also be caused by Epstein-Barr virus, herpes simplex virus, cytomegalovirus, or HIV. The second most common cause is bacterial infection of which the predominant is Group A β-hemolytic streptococcus (GABHS), which causes strep throat. Less common bacterial causes include: "Staphylococcus aureus" (including methicillin resistant Staphylococcus aureus or MRSA ),"Streptococcus pneumoniae", "Mycoplasma pneumoniae", "Chlamydia pneumoniae", "Bordetella pertussis", "Fusobacterium" sp., "Corynebacterium diphtheriae", "Treponema pallidum", and "Neisseria gonorrhoeae".

Anaerobic bacteria have been implicated in tonsillitis and a possible role in the acute inflammatory process is supported by several clinical and scientific observations.

Under normal circumstances, as viruses and bacteria enter the body through the nose and mouth, they are filtered in the tonsils. Within the tonsils, white blood cells of the immune system destroy the viruses or bacteria by producing inflammatory cytokines like phospholipase A2, which also lead to fever. The infection may also be present in the throat and surrounding areas, causing inflammation of the pharynx.

Sometimes, tonsillitis is caused by an infection of spirochaeta and treponema, in this case called Vincent's angina or Plaut-Vincent angina.

Strep throat is caused by group A beta-hemolytic streptococcus (GAS or S. pyogenes). Other bacteria such as non–group A beta-hemolytic streptococci and fusobacterium may also cause pharyngitis. It is spread by direct, close contact with an infected person; thus crowding, as may be found in the military and schools, increases the rate of transmission. Dried bacteria in dust are not infectious, although moist bacteria on toothbrushes or similar items can persist for up to fifteen days. Contaminated food can result in outbreaks, but this is rare. Of children with no signs or symptoms, 12% carry GAS in their pharynx, and, after treatment, approximately 15% of those remain positive, and are true "carriers".

Inflammatory issues associated with contact granuloma include gastroesophageal reflux, allergy or infection. There is some disagreement among researchers as to whether inflammatory issues are a direct cause. Some researchers identify reflux and infection as indirect causes due to aggressive coughing that usually occurs as a result.

First-generation antihistamine has been suggested as first-line therapy to treat post-nasal drip.

It can also be caused by certain medical conditions, such as:

- Ulcers

- Abscesses

- Upper respiratory tract infections

- Inflammation or infection of the mouth, tongue, or throat (esophagitis, pharyngitis, tonsillitis, epiglottitis)

- Immune disorders

- Oral or throat cancer

PND is suggested to be a cause of extra-oral halitosis, especially when a sinus infection is also present. Acid reflux or heartburn is believed to aggravate and in some cases cause post-nasal drip. Post-nasal drip can be a cause of laryngeal inflammation and hyperresponsiveness, leading to symptoms of vocal cord dysfunction (VCD).