Diagnosis is usually made by characteristic history and physical examination. Diagnosis can be confirmed by x-ray (80% of salivary gland calculi are visible on x-ray), by sialogram, or by ultrasound.

In one report, about 20% of individuals with mealtime syndrome had strictures upon sialography. For unknown reasons, strictures seem to be more common in females.

The differential diagnoses are extensive and include: Alagille syndrome, alpha-1-antitrypsin deficiency, Byler disease (progressive familial intrahepatic cholestasis), Caroli disease, choledochal cyst, cholestasis, congenital cytomegalovirus disease, congenital herpes simplex virus infection, congenital rubella, congenital syphilis, congenital toxoplasmosis, cystic fibrosis, galactosemia, idiopathic neonatal hepatitis, lipid storage disorders, neonatal hemochromatosis, and total parenteral nutrition-associated cholestasis.

Salivary gland atresia is congenital blockage or absence of the orifice of a major salivary gland duct or part of the duct itself.

It is a very rare condition. The submandibular salivary gland duct is usually involved, having failed to cannulate during embryological development. The condition first becomes apparent in the first few days after birth where a submandibular swelling caused by a retention cyst is noticed.

Strictures tend to be diagnosed based on difficulty with insertion and manipulation during sialendoscopy, or by sialography or ultrasound.

No treatment is required, but neoplastic processes (metastatic maliganancy to the submandibular lymph nodes and/or salivary gland tumours) should be ruled out. This is usually done with clinical exam and imaging. Very rarely, since the defect contains salivary gland tissue, salivary gland tumors can occur within an established defect but there is likely no difference in the risk of neoplasia in salivary gland tissue at other sites.

Diagnosis is made by an assessment of symptoms, physical exam, and medical history, in conjunction with blood tests, a liver biopsy, and imaging. Diagnosis is often made following investigation of prolonged jaundice that is resistant to phototherapy and/or exchange transfusions, with abnormalities in liver enzyme tests. Ultrasound or other forms of imaging can confirm the diagnosis. Further testing may include radioactive scans of the liver and a liver biopsy.

Very few risk factors for choanal atresia have been identified. While causes are unknown, both genetic and environmental triggers are suspected. One study suggests that chemicals that act as endocrine disrupters may put an unborn infant at risk. A 2012 epidemiological study looked at atrazine, a commonly used herbicide in the U.S., and found that women who lived in counties in Texas with the highest levels of this chemical being used to treat agricultural crops were 80 times more likely to give birth to infants with choanal atresia or stenosis compared to women who lived in the counties with the lowest levels. Another epidemiological report in 2010 found even higher associations between increased incidents of choanal atresia and exposure to second-hand-smoke, coffee consumption, high maternal zinc and B-12 intake and exposure to anti-infective urinary tract medications.

The histologic appearance is similar to mucoceles from other locations. The spilled mucin causes a granulation tissue to form, which usually contains foamy histiocytes. Ultrasound and magnetic resonance imaging may be useful to image the lesion. A small squamous cell carcinoma obstructing the Wharton duct may require clinical examination to be distinguished from a ranula.

Some current treatment options are:

- Non-invasive:

- For small stones, hydration, moist heat therapy, NSAIDs (nonsteroidal anti-inflammatory drugs) occasionally, and having the patient take any food or beverage that is bitter and/or sour. Sucking on citrus fruits, such as a lemon or orange, may increase salivation and promote spontaneous expulsion of the stone.

- Some stones may be massaged out by a specialist.

- Shock wave therapy (Extracorporeal shock wave lithotripsy).

- Minimally invasive:

- Sialendoscopy

- Surgical:

- An ENT or oral/maxillofacial surgeon may cannulate the duct to remove the stone (sialectomy).

- A surgeon may make a small incision near the stone to remove it.

- In some cases when stones continually reoccur the offending salivary duct is removed.

- Supporting treatment:

- To prevent infection while the stone is lodged in the duct, antibiotics are sometimes used.

Stafne's defect is usually discovered by chance during routine dental radiography. Radiographically, it is a well-circumscribed, monolocular, round, radiolucent defect, 1–3 cm in size, usually between the inferior alveolar nerve (IAN) and the inferior border of the posterior mandible between the molars and the angle of the jaw. It is one of the few radiolucent lesions that can occur below the IAN. The border is well corticated and it will have no effect on the surrounding structures. Computed tomography (CT) will show a shallow defect through the medial cortex of the mandible with a corticated rim and no soft tissue abnormalities, with the exception of a portion of the submandibular gland. Neoplasms, such as metastatic squamous cell carcinoma to the submandibular lymph nodes or a salivary gland tumour, could create a similar appearance but rarely have such well defined borders and can usually be palpated in the floor of the mouth or submandibular triangle of the neck as a hard mass. CT and clinical exam is typically sufficient to distinguish between this and a Stafne defect. The Stafne defect also tends to not increase in size or change in radiographic appearance over time (hence the term "static bone cyst"), and this can be used to help confirm the diagnosis. Tissue biopsy is not usually indicated, but if carried out, the histopathologic appearance is usually normal salivary gland tissue. Sometimes attempted biopsy of Stafne defects reveals an empty cavity (possibly because the gland was displaced at the time of biopsy), or other contents such as blood vessels, fat, lymphoid or connective tissues. Defects of the anterior lingual mandible may require biopsy for correct diagnosis at this unusual location. The radiolucent defect here may be superimposed on the lower anterior teeth and be mistaken for an odontogenic lesion. Sometimes the defect may interrupt the contour of the lower border of the mandible, and may be palpable. Sialography may be sometimes used to help demonstrate the salivary gland tissue within the bone.

A salivary gland fistula (plural "fistulae") is a fistula (i.e. an abnormal, epithelial-lined tract) involving a salivary gland or duct.

Salivary gland fistulae are almost always related to the parotid gland or duct, although the submandibular gland is rarely the origin.

The fistula can communicate with the mouth (usually causing no symptoms), the paranasal sinuses (giving rhinorrhea) or the facial skin (causing saliva to drain onto the skin).

The usual cause is trauma, however salivary fistula can occur as a complication of surgery, or if the duct becomes obstructed with a calculus.

Most parotid fistulae heal by themselves within a few weeks.

The lesion is usually present in children. Ranulas are the most common pathologic lesion associated with the sublingual glands.

A salivary diverticulum (plural "diverticuli") is a small pouch or out-pocketing of the duct system of a major salivary gland. Such diverticuli typically cause pooling of saliva and recurrent sialadenitis, especially parotitis. A diverticulum may also cause a sialolith to form.

The condition can be diagnosed by sialography. Affected individuals may "milk" the salivary gland to encourage flow of saliva through the duct.

Choanal atresia can be suspected if it is impossible to insert a nasal catheter.

Also, if one notices a continuous stream of mucus draining from one or both nostrils, it could be a sign of an atresia. Another common sign is cyanosis in an infant while breast feeding, as breathing is dependent on nasal patency in this situation.

Diagnosis is confirmed by radiological imaging, usually CT scan.

Some mucoceles spontaneously resolve on their own after a short time. Others are chronic and require surgical removal. Recurrence may occur, and thus the adjacent salivary gland is excised as a preventive measure.

Several types of procedures are available for the surgical removal of mucoceles. These include laser and minimally-invasive techniques which means recovery times are reduced drastically.

Micro-marsupialization is an alternative procedure to surgical removal. Micro-marsupialization uses silk sutures in the dome of a cyst to allow new epithelialized drainage pathways. It is simpler, less traumatic, and well-tolerated by patients, especially children.

A non-surgical option that may be effective for a small or newly identified mucocele is to rinse the mouth thoroughly with salt water (one tablespoon of salt per cup) four to six times a day for a few days. This may draw out the fluid trapped underneath the skin without further damaging the surrounding tissue. If the mucocele persists, individuals should see a doctor to discuss further treatment.

Smaller cysts may be removed by laser treatment, larger cysts will have to be removed surgically in an operating room.

Salivary gland aplasia (also termed salivary gland agenesis) is the congenital absence of salivary glands. Usually the term relates to the absence of some or all of the major salivary glands.

It is a rare condition, and most known cases have been in association with syndromes of the ectodermal tissues, particularly the lacrimal apparatus. Example syndromes which have been reported with salivary gland aplasia include hereditary ectodermal dysplasia, mandibulofacial dysostosis and hemifacial microsomia.

The main significance of the condition is a lack of saliva, causing xerostomia (dry mouth), with accompanying susceptibility to dental caries (tooth decay), infections of the mouth, and upper respiratory tract infections (e.g., candidiasis, ascending sialadenitis, laryngitis and pharyngitis). Patients with salivary gland aplasia typically require regular application of topical fluoride to prevent tooth decay.

Standard, and most effective, therapy to date is glandular sialadenectomy, which is associated with fairly low operative morbidity; however, in recent times, the administration of steroid (which can shrink the inflammatory lesion and is known to reduce serum IgG4 values) has been considered favorably, and may be useful in younger patients or those who refuse surgery.

Differentiation between this and SCC would be based on a history of recent trauma or dental treatment in the area.

Immunohistochemistry may aid the diagnosis. If the lesion is NS, there will be focal to absent immunoreactivity for p53, low immunoreactivity for MIB1 (Ki-67), and the presence of 4A4/p63- and calponin-positive myoepithelial cells.

There are many diagnostic methods that can be used to determine the type of salivary gland tumour and if it is benign or malignant. Examples of diagnostic methods include:

Physical exam and history: An exam of the body to check general signs of health. The head, neck, mouth, and throat will be checked for signs of disease, such as lumps or anything else that seems unusual. A history of the patient's health habits and past illnesses and treatments will also be taken.

Endoscopy: A procedure to look at organs and tissues inside the body to check for abnormal areas. For salivary gland cancer, an endoscope is inserted into the mouth to look at the mouth, throat, and larynx. An endoscope is a thin, tube-like instrument with a light and a lens for viewing.

MRI

Biopsy: The removal of cells or tissues so they can be viewed under a microscope by a pathologist to check for signs of cancer.

Fine needle aspiration (FNA) biopsy: The removal of tissue or fluid using a thin needle. An FNA is the most common type of biopsy used for salivary gland cancer, and has been shown to produce accurate results when differentiating between benign and malignant tumours.

Radiographs: An OPG (orthopantomogram) can be taken to rule out mandibular involvement. A chest radiograph may also be taken to rule out any secondary tumours.

Ultrasound: Ultrasound can be used to initially assess a tumour that is located superficially in either the submandibular or parotid gland. It can distinguish an intrinsic from an extrinsic neoplasm. Ultrasonic images of malignant tumours include ill defined margins.

Both mucous retention and extravasation phenomena are classified as salivary gland disorders.

Ectopic salivary gland tissue which is located in sites other than the normal location is variously described as aberrant, accessory, ectopic, heterotopic or salivary gland choristoma.

This condition takes several different forms, often involving one or more fistulas connecting the trachea to the esophagus (tracheoesophageal fistula).

Given the difficulties of a definitive pre-operative diagnosis, the clinical entity of Küttner's tumor has so far remained significantly under-reported and under-recognized. In recent times, armed with a better understanding of the occurrences and observable features of this condition, surgeons are increasingly depending upon pre-operative ultrasonography along with Fine-needle aspiration cytological (FNAC) examinations to make an accurate presumptive diagnosis, and according to one estimate, about 44% of patients undergoing submandibular resection are found to have this condition. In the ultrasonogram, Küttner's tumor is characterized by a diffuse, heterogeneous zone of echo-shadows. The FNAC finds cells greatly reduced in number (called 'paucicellularity') along with scattered tubular ducts against a backdrop of lymphoplasmacytic infiltration and fibrous depositions. There may be a reduced but moderate number of cells and ducts enveloped in fibrous sheaths, as well as fibrous proliferation of the gland's septa. The cytologic findings by themselves may not be specific, and the diagnosis requires adjunct consideration of both the ultrasonogram and clinical presentation. Application of magnetic resonance imaging (MRI) has been tried to non-invasively examine the morphological variations in Küttner's tumor and differentiate them from those seen in malignant tumors; while MRI findings of the affected tissue and the pattern of cellular infiltration may offer some diagnostic clues for this condition, so far the results have been inconclusive.

This condition may be visible, after about 26 weeks, on an ultrasound. On antenatal USG, the finding of an absent or small stomach in the setting of polyhydramnios was considered a potential symptom of esophageal atresia. However, these findings have a low positive predictive value. The upper neck pouch sign is another sign that helps in the antenatal diagnosis of esophageal atresia and it may be detected soon after birth as the affected infant will be unable to swallow its own saliva. Also, the newborn can present with gastric distention, cough, apnea, tachypnea, and cyanosis. In many types of esophageal atresia, a feeding tube will not pass through the esophagus.