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.

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

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.

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).

Viruses that may cause adenoiditis include adenovirus, rhinovirus and paramyxovirus. Bacterial causes include Streptococcus pyogenes, Streptococcus pneumoniae, Moraxella catarrhalis and various species of Staphylococcus including Staphylococcus aureus.

Adenoiditis occurs mainly in childhood, often associated with acute tonsillitis. Incidence decreases with age, with adenoiditis being rare in children over 15 years due to physiological atrophy of the adenoid tissue.

It has been hypothesized that biofilm bacterial infections may account for many cases of antibiotic-refractory chronic sinusitis. Biofilms are complex aggregates of extracellular matrix and inter-dependent microorganisms from multiple species, many of which may be difficult or impossible to isolate using standard clinical laboratory techniques. Bacteria found in biofilms have their antibiotic resistance increased up to 1000 times when compared to free-living bacteria of the same species. A recent study found that biofilms were present on the mucosa of 75% of people undergoing surgery for chronic sinusitis.

It is a commonly encountered otorhinolaryngological (ENT) emergency.

The number of new cases per year of peritonsillar abscess in the United States has been estimated approximately at 30 cases per 100,000 people. In a study in Northern Ireland, the number of new cases was 10 cases per 100,000 people per year.

In Denmark, the new number of new cases is higher and reaches 41 cases per 100,000 people per year. Younger children who develop a peritonsillar abscess are often immunocompromised and in them, the infection can cause airway obstruction.

Acute sinusitis is usually precipitated by an earlier upper respiratory tract infection, generally of viral origin, mostly caused by rhinoviruses, coronaviruses, and influenza viruses, others caused by adenoviruses, human parainfluenza viruses, human respiratory syncytial virus, enteroviruses other than rhinoviruses, and metapneumovirus. If the infection is of bacterial origin, the most common three causative agents are "Streptococcus pneumoniae", "Haemophilus influenzae", and "Moraxella catarrhalis". Until recently, "Haemophilus influenzae" was the most common bacterial agent to cause sinus infections. However, introduction of the "H. influenza" type B (Hib) vaccine has dramatically decreased "H. influenza" type B infections and now non-typable "H. influenza" (NTHI) are predominantly seen in clinics. Other sinusitis-causing bacterial pathogens include "Staphylococcus aureus" and other streptococci species, anaerobic bacteria and, less commonly, gram negative bacteria. Viral sinusitis typically lasts for 7 to 10 days, whereas bacterial sinusitis is more persistent. Approximately 0.5% to 2% of viral sinusitis results in subsequent bacterial sinusitis. It is thought that nasal irritation from nose blowing leads to the secondary bacterial infection.

Acute episodes of sinusitis can also result from fungal invasion. These infections are typically seen in patients with diabetes or other immune deficiencies (such as AIDS or transplant patients on immunosuppressive anti-rejection medications) and can be life-threatening. In type I diabetics, ketoacidosis can be associated with sinusitis due to mucormycosis.

Chemical irritation can also trigger sinusitis, commonly from cigarette smoke and chlorine fumes. Rarely, it may be caused by a tooth infection.

PTA usually arises as a complication of an untreated or partially treated episode of acute tonsillitis. The infection, in these cases, spreads to the peritonsillar area (peritonsillitis). This region comprises loose connective tissue and is hence susceptible to formation of an abscess. PTA can also occur "". Both aerobic and anaerobic bacteria can be causative. Commonly involved aerobic pathogens include "Streptococcus, Staphylococcus" and "Haemophilus". The most common anaerobic species include "Fusobacterium necrophorum", " Peptostreptococcus", "Prevotella species", and "Bacteroides".

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.

In terms of pathophysiology, rhino virus infection resembles the immune response. The viruses do not cause damage to the cells of the upper respiratory tract but rather cause changes in the tight junctions of epithelial cells. This allows the virus to gain access to tissues under the epithelial cells and initiate the innate and adaptive immune responses.

Up to 15% of acute pharyngitis cases may be caused by bacteria, most commonly "Streptococcus pyogenes", a group A streptococcus in streptococcal pharyngitis ("strep throat"). Other bacterial causes are "Streptococcus pneumoniae", "Haemophilus influenzae", "Corynebacterium diphtheriae", "Bordetella pertussis", and "Bacillus anthracis".

Sexually transmitted infections have emerged as causes of oral and pharyngeal infections.

The exact length of time between infection and symptoms is unclear. A review of the literature made an estimate of 33–49 days. In adolescents and young adults, symptoms are thought to appear around 4–6 weeks after initial infection. Onset is often gradual, though it can be abrupt. The main symptoms may be preceded by 1–2 weeks of fatigue, feeling unwell and body aches.

About 90% of cases of infectious mononucleosis are caused by the Epstein–Barr virus, a member of the Herpesviridae family of DNA viruses. It is one of the most commonly found viruses throughout the world. Contrary to common belief, the Epstein–Barr virus is not highly contagious. It can only be contracted through direct contact with an infected person’s saliva, such as through kissing or sharing toothbrushes, cups, etc. About 95% of the population has been exposed to this virus by the age of 40, but only 15–20% of teenagers and about 40% of exposed adults actually become infected.

In chronic recurrent sialadenitis or chronic sclerosing sialadenitis, acute attacks are managed with conservative therapies such as hydration, analgesics (mainly NSAIDs), sialogogues to stimulate salivary secretion, and regular, gentle gland massage. If infection is present, appropriate cultures should be obtained, followed by empirical antibiotic therapy initially, for example amoxicillin/clavulanate or clindamycin which cover oral flora.

If there are attacks more than approximately 3 times per year or severe attacks, surgical excision of the affected gland should be considered.

Typically spreads via the fecal-oral route or via respiratory droplets.

Herpangina, also called mouth blisters, is a painful mouth infection caused by coxsackieviruses. Usually, herpangina is produced by one particular strain of coxsackie virus A (and the term "herpangina virus" refers to coxsackievirus A) but it can also be caused by coxsackievirus B or echoviruses. Most cases of herpangina occur in the summer, affecting mostly children. However, it occasionally occurs in adolescents and adults. It was first characterized in 1920.

Catarrh , or catarrhal inflammation, is inflammation of the mucous membranes in one of the airways or cavities of the body, usually with reference to the throat and paranasal sinuses. It can result in a thick exudate of mucus and white blood cells caused by the swelling of the mucous membranes in the head in response to an infection. It is a symptom usually associated with the common cold, pharyngitis, and chesty coughs, but it can also be found in patients with adenoiditis, otitis media, sinusitis or tonsillitis. The phlegm produced by catarrh may either discharge or cause a blockage that may become chronic.

The word "catarrh" was widely used in medicine since before the era of medical science, which explains why it has various senses and in older texts may be synonymous with, or vaguely indistinguishable from, common cold, nasopharyngitis, pharyngitis, rhinitis, or sinusitis. The word is no longer as widely used in American medical practice, mostly because more precise words are available for any particular pathosis. Indeed, to the extent that it is still used, it is no longer viewed nosologically as a disease entity but instead as a symptom, a sign, or a syndrome of both. The term "catarrh" is found in medical sources from the United Kingdom. The word has also been common in the folk medicine of Appalachia, where medicinal plants have been used to treat the inflammation and drainage associated with the condition.

Chronic bacterial prostatitis is a relatively rare condition that usually presents with an intermittent UTI-type picture. It is defined as recurrent urinary tract infections in men originating from a chronic infection in the prostate. Symptoms may be completely absent until there is also bladder infection, and the most troublesome problem is usually recurrent cystitis.

Chronic bacterial prostatitis occurs in less than 5% of patients with prostate-related non-BPH lower urinary tract symptoms (LUTS).

Dr. Weidner, Professor of Medicine, Department of Urology, University of Gießen, has stated: "In studies of 656 men, we seldom found chronic bacterial prostatitis. It is truly a rare disease. Most of those were E-coli."

Sialadenitis (sialoadenitis) is inflammation of a salivary gland. It may be subdivided temporally into acute, chronic and recurrent forms.

Chronic bacterial prostatitis is a bacterial infection of the prostate gland. It should be distinguished from other forms of prostatitis such as acute bacterial prostatitis and chronic pelvic pain syndrome (CPPS).

Due to the human ear's function of regulating the pressure within the head region, catarrh blockage may cause discomfort during changes in atmospheric pressure.

Tonsilloliths or tonsillar concretions occur in up to 10% of the population, frequently due to episodes of tonsillitis. While small concretions in the tonsils are common, true tonsilloliths or stones are rare. They commonly occur in young adults and are rare in children.

Otitis media is a particularly common cause of otalgia in early childhood, often occurring secondary to other infectious illnesses, such as colds, coughs, or conjunctivitis.

The mechanism by which these calculi form is subject to debate, though they appear to result from the accumulation of material retained within the crypts, along with the growth of bacteria and fungi – sometimes in association with persistent chronic purulent tonsillitis.

Recently, an association between biofilms and tonsilloliths was shown. Central to the biofilm concept is the assumption that bacteria form a three dimensional structure, dormant bacteria being in the center to serve as a constant nidus of infection. This impermeable structure renders the biofilm immune to antibiotic treatment. By use of confocal microscopy and microelectrodes, biofilms similar to dental biofilms were shown to be present in the tonsillolith, with oxygen respiration at the outer layer of tonsillolith, denitrification toward the middle, and acidification toward the bottom.