A common symptom of laryngeal papillomatosis is a perceptual change in voice quality. More specifically, hoarseness is observed. As a consequence of the narrowing of the laryngeal or tracheal parts of the airway, shortness of breath, chronic cough and stridor (i.e. noisy breathing which can sound like a whistle or a snore), can be present. As the disease progresses, occurrence of secondary symptoms such as dysphagia, pneumonia, acute respiratory distress syndrome, failure to thrive, and recurrent upper respiratory infections can be diagnosed. In children, symptoms are usually more severe and often mistaken for manifestations of other diseases such as asthma, croup or bronchitis. Therefore, diagnosis is usually delayed.

Laryngeal papillomatosis, also known as recurrent respiratory papillomatosis, is a rare medical condition that leads to audible changes in voice quality and narrowing of the airway. It is caused by type 6 and 11 human papillomavirus (HPV) infections of the throat, in which benign tumors or papillomas form on the larynx or other areas of the respiratory tract. Laryngeal papillomatosis is initially diagnosed through indirect laryngoscopy upon observation of growths on the larynx and can be confirmed through a biopsy. Treatment for laryngeal papillomatosis aims to remove the papillomas and limit their recurrence. Due to the recurrent nature of the virus, repeated treatments usually are needed. Laryngeal papillomatosis is primarily treated surgically, though supplemental nonsurgical and/or medical treatments may be considered in some cases. The evolution of laryngeal papillomatosis is highly variable. Though total recovery may be observed, it is often persistent despite treatment. The number of new cases of laryngeal papillomatosis cases is at approximately 4.3 cases per 100 000 children and 1.8 cases per 100 000 adults annually.

The differential of TO includes amyloidosis, which is typically circumferential, papillomatosis, though this usually occurs in younger patients and can cause lung cavitation when disseminated, granulomatosis with polyangiitis, though this is circumferential as well and often involves distal lung cavitation as well. Relapsing polychondritis can also spare the posterior wall, though it is not typically nodular in appearance.

Florid cutaneous papillomatosis (also known as the Schwartz-Burgess syndrome) is an obligate paraneoplastic syndrome.

FCP begins as the sudden onset of numerous cutaneous papillomas that are clinically indistinguishable from viral warts. The papillomas range from 1 to 3 mm in diameter may spread to involve the entire body, including the face. Pruritus, which may sometimes precede the onset of FCP, is evident in the affected regions in about half of patients. Evaluation of a skin biopsy clearly distinguishes FCP from viral warts.

FCP is associated with underlying cancer of the breast, bladder, ovary, uterus, prostate, and lung. Other associated underlying malignancies include squamous cell carcinomas and lymphomas such as non-Hodgkin's lymphoma.

FCP is sometimes seen together with other signs of internal cancer, especially malignant acanthosis nigricans, tripe palms, Leser–Trélat sign, and hypertrichosis lanuginosa acquisita. FCP tends to improve in association with surgical or chemotherapeutic therapy of the underlying internal cancer. A recurrence or exacerbation of FCP may be linked with tumor regrowth or metastatic spread.

Tracheobronchopathia osteochondroplastica (TO) is a rare benign disease of unknown cause, in which multiple cartilaginous or bony submucosal nodules project into the trachea and proximal bronchi. The nodules usually spare the posterior wall of the airway because they are of cartilaginous origin, while the posterior wall of the airway is membranous (does not contain cartilage). This is as opposed to tracheobronchial amyloidosis, which does not spare the posterior wall.

It usually occurs in men around their fifth decade of life, as opposed to tracheobronchial papillomatosis due to HPV infection, which usually occurs in younger patients. TO can cause airway obstruction, bleeding and chronic cough. Treatment involves the use of bronchodilators, and physical dilatation by bronchoscopy. The patients are also more prone to post-obstructive pneumonia and chronic lung infection in severe cases.

Oral florid papillomatosis is a condition characterized by a white mass resembling a cauliflower covering the tongue and extending onto other portions of the mucous membranes. This is a type of verrucous carcinoma.

The characteristic eruption is of multiple warty papules and nodules beginning on acral skin, especially the hands and wrists, and disseminating onto the skin of the entire body. These skin lesions develop on the trunk, extremities, and face, and are almost twice as common in men than in women, especially individuals aged 53–72 years. Pruritus is also associated.

Extraesophageal symptoms result from exposure of the upper aerodigestive tract to gastric contents. This causes a variety of symptoms, including hoarseness, postnasal drip, sore throat, difficulty swallowing, indigestion, chronic cough, wheezing, globus pharyngeus, and chronic throat-clearing. Some people with LPR have heartburn, while others have little to no heartburn as refluxed stomach contents do not remain in the esophagus long enough to irritate the surrounding tissue. Individuals with more severe forms of LPR may experience abrasion of tooth enamel due to intermittent presence of gastric contents in the oral cavity.

Additionally, LPR can cause inflammation in the vocal tract which results in the symptom of dysphonia or hoarseness. Hoarseness is considered to be one of the primary symptoms of LPR and is associated with complaints such as strain, vocal fatigue, muskuloskeletal tension, and hard glottal attacks, all of which can reduce a person's ability to communicate effectively. Moreover, LPR patients may try to compensate for their hoarseness by increasing muscular tension in their vocal tract. This hyper-functional technique adopted in response to the inflammation caused by LPR can lead to a condition called muscle tension dysphonia and may persist even after the hoarseness and inflammation has disappeared. A speech-language pathologist will often need to be involved to help resolve this maladaptive, compensatory pattern through the implementation of voice therapy.

LPR presents as a chronic and intermittent disease in children. LPR in children and infants tends to manifest with a unique set of symptoms. Symptoms seen in children with LPR include a cough, hoarseness, stridor, sore throat, asthma, vomiting, globus sensation, wheezing, aspiration and recurrent pneumonia. Common symptoms of LPR in infants include wheezing, stridor, persistent or recurrent cough, apnea, feeding difficulties, aspiration, regurgitation, and failure to thrive. Moreover, LPR in children is commonly concomitant with laryngeal disorders such as laryngomalacia, subglottic stenosis, and laryngeal papillomatosis.

Many of the symptoms are not limited to the disorder, as they may resemble a number of conditions that affect the upper and lower airway. Such conditions include asthma, angioedema, vocal cord tumors, and vocal cord paralysis.

People with vocal cord dysfunction often complain of "difficulty in breathing in” or “fighting for breath”, which can lead to subjective respiratory distress, and in severe cases, loss of consciousness. They may report tightness in the throat or chest, choking, stridor on inhalation and wheezing, which can resemble the symptoms of asthma. These episodes of dyspnea can be recurrent and symptoms can range from mild to severe and prolonged in some cases. Agitation and a sense of panic are not uncommon and can result in hospitalization.

Different subtypes of vocal cord dysfunction are characterized by additional symptoms. For instance, momentary aphonia can be caused by laryngospasm, an involuntary spasm of the vocal cords and a strained or hoarse voice may be perceived when the vocal cord dysfunction occurs during speech, resulting in spasmodic dysphonia.

Many of the symptoms are not specific to vocal cord dysfunction and can resemble a number of conditions that affect the upper and lower airway.

A URI may be classified by the area inflamed.

Rhinitis affects the nasal mucosa, while rhinosinusitis or sinusitis affects the nose and paranasal sinuses, including frontal, ethmoid, maxillary, and sphenoid sinuses. Nasopharyngitis (rhinopharyngitis or the common cold) affects the nares, pharynx, hypopharynx, uvula, and tonsils generally. Without involving the nose, pharyngitis inflames the pharynx, hypopharynx, uvula, and tonsils. Similarly, epiglottitis (supraglottitis) inflames the superior portion of the larynx and supraglottic area; laryngitis is in the larynx; laryngotracheitis is in the larynx, trachea, and subglottic area; and tracheitis is in the trachea and subglottic area.

Tracheobronchomegaly is a very rare congenital disorder of the lung primarily characterized by an abnormal widening of the upper airways. The abnormally widened trachea and mainstem bronchi are associated with recurrent lower respiratory tract infection and copious purulent sputum production, eventually leading to bronchiectasis and other respiratory complications.

Woodring et al. (1991) suggested the following diagnostic criteria for tracheomegaly in adults based on chest radiography:

- Adult Males: Tracheal transverse diameter > 25 mm and sagittal diameter > 27 mm.

- Adult Females: Tracheal transverse diameter > 21 mm and sagittal diameter > 23 mm.

Bronchomalacia can best be described as a birth defect of the bronchus in the respiratory tract. Congenital malacia of the large airways is one of the few causes of irreversible airways obstruction in children, with symptoms varying from recurrent wheeze and recurrent lower airways infections to severe dyspnea and respiratory insufficiency. It may also be acquired later in life due to chronic or recurring inflammation resulting from infection or other airway disease.

Bronchomalacia is a term for weak cartilage in the walls of the bronchial tubes, often occurring in children under six months. Bronchomalacia means 'floppiness' of some part of the bronchi. Patients present with noisy breathing and/or wheezing. There is collapse of a main stem bronchus on exhalation. If the trachea is also involved the term tracheobronchomalacia (TBM) is used. If only the upper airway the trachea is involved it is called tracheomalacia (TM). There are two types of bronchomalacia. Primary bronchomalacia is due to a deficiency in the cartilaginous rings. Secondary bronchomalacia may occur by extrinsic compression from an enlarged vessel, a vascular ring or a bronchogenic cyst. Though uncommon, idiopathic (of unknown cause) tracheobronchomalacia has been described in older adults.

In uncomplicated colds, cough and nasal discharge may persist for 14 days or more even after other symptoms have resolved.

Acute upper respiratory tract infections include rhinitis, pharyngitis/tonsillitis and laryngitis often referred to as a common cold, and their complications: sinusitis, ear infection and sometimes bronchitis (though bronchi are generally classified as part of the lower respiratory tract.) Symptoms of URTIs commonly include cough, sore throat, runny nose, nasal congestion, headache, low-grade fever, facial pressure and sneezing.

Symptoms of rhinovirus in children usually begin 1–3 days after exposure. The illness usually lasts 7–10 more days.

Color or consistency changes in mucous discharge to yellow, thick, or green are the natural course of viral upper respiratory tract infection and not an indication for antibiotics.

Group A beta hemolytic streptococcal pharyngitis/tonsillitis (strep throat) typically presents with a sudden onset of sore throat, pain with swallowing and fever. Strep throat does not usually cause runny nose, voice changes, or cough.

Pain and pressure of the ear caused by a middle ear infection (otitis media) and the reddening of the eye caused by viral conjunctivitis are often associated with upper respiratory infections.

"Episodes" can be triggered suddenly or develop gradually and triggers are numerous. Primary causes are believed to be gastroesophageal reflux disease (GERD), extra-esophageal reflux (EERD), exposure to inhaled allergens, post-nasal drip, exercise, or neurological conditions that can cause difficulty inhaling only during waking. Published studies emphasize anxiety or stress as a primary cause while more recent literature indicates a likely physical etiology. This disorder has been observed from infancy through old age, with the observation of its occurrence in infants leading some to believe that a physiological cause such as reflux or allergy is likely. Certain medications, such as antihistamines for allergies, cause drying of the mucous membranes, which can cause further irritation or hypersensitivity of the vocal cords.VCD can mimic asthma, anaphylaxis, collapsed lungs, pulmonary embolism, or fat embolism, which can lead to an inaccurate diagnosis and inappropriate, potentially harmful, treatment. Some incidences of VCD are misdiagnosed as asthma, but are unresponsive to asthma therapy, including bronchodilators and steroids. Among adult patients, women tend to be diagnosed more often. Among children and teenage patients, VCD has been linked with high participation in competitive sports and family orientation towards high achievement.

Vocal cord dysfunction co-occurs with asthma approximately 40% of the time. This frequently results in a misdiagnosis of asthma alone. Even young children can tell the difference between an asthma attack (primarily difficulty exhaling) and a VCD attack (primarily difficulty inhaling). Knowing the difference between the two will help those who have both know when to use the rescue inhaler prescribed or when to use the breathing recovery exercises trained by a speech-language pathologist.

The disease has a long incubation period, and therefore signs usually occur in adult animals (over 2 years of age). Clinical signs resemble a non-specific progressive pneumonia, including poor body condition and, particularly after exercise, respiratory difficulty. Unless a concurrent lung infection is present, affected sheep continue to eat. The only sign specific to OPA is a watery nasal discharge, consisting of lung fluid produced by the affected lung tissue; lifting the hind legs of the animal above the level of its head will cause large volumes of this fluid to flow from the nostrils.

There are no reliable tests for the diagnosis of OPA in live animals which are suitable for use on farms, so diagnosis can only be confirmed at necropsy (post-mortem examination). On necropsy, lungs are interspersed with multifocal tumors. Some of these are small discrete nodules and others will involve the entire half of a lung lobule. JSRV acutely transforms the lung epithelia into cancerous cells, with type-2 pneumocytes and club cells being the likely target for JSRV transformation. The tumors have overactive secretory functions, which are a hallmark of OPA.

The retroviral antigen levels of JSRV are very high in OPA tumors and can be detected in the lung secretions of infected sheep. It is thought that infected animals secrete the virus before showing signs, so the virus is easily spread within flocks.

LPR is often regarded as a subtype of GERD that occurs when stomach contents flow upward through the esophagus and reach the level of the larynx and pharynx. However, LPR is associated with a distinct presentation of symptoms. LPR and GERD frequently differ in the relative prevalence of heartburn and throat clearing. While heartburn is present in over 80% of GERD cases, it occurs in only 20% of LPR cases. Throat clearing shows the opposite prevalence pattern, occurring in approximately 87% of LPR cases and in fewer than 5% of GERD cases. Unlike GERD, LPR also poses a risk for bronchitis or pneumonitis as reflux of stomach acid to the level of the larynx can result in aspiration. LPR is also commonly associated with erythema, or redness, as well as edema in the tissues of the larynx that are exposed to gastric contents. In contrast, most cases of GERD are nonerosive, with no apparent injury to the mucosal lining of the esophageal tissue exposed to the refluxed material.

Differences in the molecular structure of the epithelial tissue lining the laryngopharyngeal region may be partly responsible for the different symptomatic manifestations of LPR in comparison to GERD. In contrast to the resistant stratified squamous epithelium lining the esophagus, the larynx is lined by ciliated respiratory epithelium, which is more fragile and susceptible to damage. While the epithelium lining the esophagus is capable of withstanding as many as 50 instances of exposure to gastric contents each day, which is the uppermost estimate considered to be within the range of normal physiologic functioning, injury to laryngeal epithelium can occur following exposure to only small amounts of acidic gastric contents.

Ovine pulmonary adenocarcinoma (OPA), also known as ovine pulmonary adenomatosis, or jaagsiekte, is a chronic and contagious disease of the lungs of sheep and goats. OPA is caused by a retrovirus called jaagsiekte sheep retrovirus (JSRV).

Feeding and swallowing can become difficult for people with A-T as they get older. Feeding refers to all aspects of eating and drinking, including getting food and liquids to the mouth; swallowing refers to ingestion or what happens after food or liquids enter the mouth. Primary goals for feeding and swallowing are safe, adequate, and enjoyable mealtimes.

Involuntary movements may make feeding difficult or messy and may excessively prolong mealtimes. It may be easier to finger feed than use utensils (e.g., spoon or fork). For liquids, it is often easier to drink from a closed container with a straw than from an open cup. Caregivers may need to provide foods or liquids so that self-feeding is possible, or they may need to feed the person with A-T. In general, meals should be completed within approximately 30 minutes. Longer meals may be stressful, interfere with other daily activities, and limit the intake of necessary liquids and nutrients.

If swallowing problems (dysphagia) occur, they typically present during the second decade of life. Dysphagia is common because of the neurological changes that interfere with coordination of mouth and pharynx (throat) movements that are needed for safe and efficient swallowing. Coordination problems involving the mouth may make chewing difficult and increase the duration of meals. Problems involving the pharynx may cause liquid, food, and saliva to be inhaled into the airway (aspiration). People with dysphagia may not cough when they aspirate (silent aspiration). Swallowing problems and especially swallowing problems with silent aspiration may cause lung problems due to inability to cough and clear food and liquids from the airway.

- Warning signs of a swallowing problem

- Choking or coughing when eating or drinking

- Poor weight gain (during ages of expected growth) or weight loss at any age

- Excessive drooling

- Mealtimes longer than 40 – 45 minutes, on a regular basis

- Foods or drinks previously enjoyed are now refused or difficult

- Chewing problems

- Increase in the frequency or duration of breathing or respiratory problems

- Increase in lung infections

Papillomatosis cutis carcinoides (also known as "Gottron's carcinoid papillomatosis" and "Papillomatosis cutis carcinoides of Gottron–Eisenlohr") is a cutaneous condition characterized by verrucous skin lesions, and is due to an HPV infection of the skin.

Voice disorders are medical conditions involving abnormal pitch, loudness or quality of the sound produced by the larynx and thereby affecting speech production. These include:

- Puberphonia

- Chorditis

- Vocal fold nodules

- Vocal fold cysts

- Vocal cord paresis

- Reinke's edema

- Spasmodic dysphonia

- Foreign accent syndrome

- Bogart–Bacall syndrome

- Laryngeal papillomatosis

- Laryngitis

Skin infection ("cutaneous" infection) with HPV is very widespread.

Skin infections with HPV can cause noncancerous skin growths called warts (verrucae). Warts are caused by a rapid growth of cells on the outer layer of the skin.

While cases of warts have been described since the time of ancient Greece, their viral cause was not known until 1907.

Skin warts are most common in childhood and typically appear and regress spontaneously over the course of weeks to months. About 10% of adults also suffer from recurring skin warts. All HPVs are believed to be capable of establishing long-term "latent" infections in small numbers of stem cells present in the skin. Although these latent infections may never be fully eradicated, immunological control is thought to block the appearance of symptoms such as warts. Immunological control is HPV type-specific, meaning an individual may become resistant to one HPV type while remaining susceptible to other types. In one study, infection by HPV types 2, 27, and 57 was found in people with warts, while infection by HPV types 1, 2, 63, and 27 was found in people with clinically normal skin.

Types of warts include:

- Common warts are usually found on the hands and feet, but can also occur in other areas, such as the elbows or knees. Common warts have a characteristic cauliflower-like surface and are typically slightly raised above the surrounding skin. Cutaneous HPV types can cause genital warts but are not associated with the development of cancer.

- Plantar warts are found on the soles of the feet; they grow inward, generally causing pain when walking.

- Subungual or periungual warts form under the fingernail (subungual), around the fingernail, or on the cuticle (periungual). They are more difficult to treat than warts in other locations.

- Flat warts are most commonly found on the arms, face, or forehead. Like common warts, flat warts occur most frequently in children and teens. In people with normal immune function, flat warts are not associated with the development of cancer.

Genital warts are quite contagious, while common, flat, and plantar warts are much less likely to spread from person to person.

Tracheoesophageal fistula is suggested in a newborn by copious salivation associated with choking, coughing, vomiting, and cyanosis coincident with the onset of feeding. Esophageal atresia and the subsequent inability to swallow typically cause polyhydramnios in utero. Rarely it may present in an adult.

Surgical repair can sometimes result in complications, including:

- Stricture, due to gastric acid erosion of the shortened esophagus

- Leak of contents at the point of anastomosis

- Recurrence of fistula

- Gastro-esophageal reflux disease

- Dysphagia

- Asthma-like symptoms, such as persistent coughing/wheezing

- Recurrent chest infections

- Tracheomalacia