Ultrasound is the often chosen to examine the duct and determine the presence and size of any cysts or abnormalities. Fine-needle aspiration cytology can also be used to confirm the diagnosis.

In order to prevent further cysts and infections from forming, the thyroglossal duct and all of its branches are removed from the throat and neck area. A procedure, known as the Sistrunk procedure, is considered to be the standard procedure and involves removal of portions of the hyoid bone and core tissue of the suprahyoid region. Cysts will often reoccur if the entire duct is not removed, so reoccurrence requires a wider range of tissue to be removed in a subsequent surgery.

Delaying the surgical procedure almost always leads to recurrent infections, which will continue to delay the needed treatment. The Sistrunk procedure has a reoccurrence rate of less than 5%, proving it is extremely effective at removing the majority of traces of the persistent thyroglossal duct.

Clinical features can be found in the subhyoid portion of the tract and 75% present as midline swellings. The remainder can be found as far lateral as the lateral tip of the hyoid bone.

Typically, the cyst will move upwards on protrusion of the tongue, given its attachment to the embryonic duct, as well as on swallowing, due to attachment of the tract to the foramen caecum.

Diagnosis of a thyroglossal duct cyst requires a medical professional, and is usually done by a physical examination. It is important to identify whether or not the thyroglossal cyst contains any thyroid tissue, as it can define the degree of cyst that is being dealt with.

Diagnostic procedures for a thyroglossal cyst include:

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.

Evaluation is in the form of a dye disappearance test followed by irrigation test. By using this sequence (with modifications) as a guide, the physician can frequently streamline diagnostic testing.

The most common and accurate way of diagnosing an individual with this anomaly is by MRCP (Magnetic Resonance Cholangiopancreatography) or ERCP (Endoscopic Retrograde Cholangiopancreatography). This test can demonstrate the presence of two separately draining ducts within the pancreas. Other tests can assist doctors with diagnosis, such as a CT scan and an MRI.

The dye disappearance test (DDT) is useful for assessing the presence or absence of adequate lacrimal outflow, especially in unilateral cases. It is more heavily relied upon in children, in whom lacrimal irrigation is impossible without deep sedation. Using a drop of sterile 2% fluorescein solution or a moistened fluorescein strip, the examiner instills fluorescein into the conjunctival fornices of each eye and then observes the tear film, preferably with the cobalt blue filter of the slit lamp. Persistence of significant dye and, particularly asymmetric clearance of the dye from the tear meniscus over a 5-minute period indicate an obstruction. If the DDT result is normal, severe lacrimal drainage dysfunction is highly unlikely. Variations of the DDT are the Jones tests.

Cysts from 1–5 mm on CT or ultrasound are typically too small to characterize and considered benign. No further imaging follow-up is recommended for these lesions. Cysts from 6–9 mm require a single follow-up in 2–3 years, preferably with MRCP to better evaluate the pancreatic duct. If stable at follow-up, no further imaging follow-up is recommended. For cysts from 1–1.9 cm follow-up is suggested with MRCP or multiphasic CT in 1–2 years. If stable at follow-up, the interval of imaging follow-up is increased to 2–3 years. Cysts from 2–2.9 cm have more malignant potential, and a baseline endoscopic ultrasound is suggested, followed by MRCP or multiphasic CT in 6–12 months. If patients are young, surgery may be considered to avoid the need for prolonged surveillance. If these cysts are stable at follow-up, interval imaging follow-up can be done in 1–2 years.

The condition is usually self-limiting, and thus not indicated for surgery.

Imaging by ultrasonography, MRCP, or CT scan usually make the diagnosis. MRCP can be used to define the lesion anatomically prior to surgery.

Occasionally Mirizzi's syndrome is diagnosed or confirmed on ERCP when requested to alleviate obstructive jaundice or cholangitis by means of an endoscopically placed stent, or when USS has been wrongly reported as choledocolithiasis.

Timo cysts may spontaneously resolve or with pressure directed toward the nose; however, nasolacrimal duct probing may be required to open the obstruction.

The term "duct ectasia syndrome" has been used to describe symptoms of nonpuerperal mastitis, possibly associated with nipple inversion and nipple discharge. In some contexts, it was used to describe a particular form of nonpuerperal mastitis coincident with fibrocystic disease, frequently involving pasty (coloured) nipple discharge, nipple retraction, retroareolar abscess and blue dome cysts. Abscessation is not very frequent but by some definitions recurrent subareolar abscess is merely a variant of duct ectasia syndrome - abscessation would be obviously more frequent with this definition.

Duct ectasia syndrome has been associated with histopathological findings that are distinct from a simple duct widening. In addition to nonspecific duct widening the myoepithelial cell layer is atrophic, missing or replaced by fibrous tissue. The original cuboidal epithelial layer may be also severely impaired or missing. Characteristic calcifications are often visible on mammographic images.

Periductal mastitis, comedo mastitis, secretory disease of the breast, plasma cell mastitis and mastitis obliterans are sometimes considered special cases or synonyms of duct ectasia syndrome.

Other conditions that may present similarly include hidradenoma papilliferum, lipomas, epidermoid cysts and Skene's duct cysts among others. In those who are more than 40 years of age a biopsy may be recommended to ensure cancer is not present.

Diagnostic workup varies by the stone type, but in general:

- Clinical history and physical examination

- Imaging studies

- Some stone types (mainly those with substantial calcium content) can be detected on X-ray and CT scan

- Many stone types can be detected by ultrasound

- Factors contributing to stone formation (as in #Etiology) are often tested:

- Laboratory testing can give levels of relevant substances in blood or urine

- Some stones can be directly recovered (at surgery, or when they leave the body spontaneously) and sent to a laboratory for analysis of content

Nasopalatine duct cysts usually present as asymptomatic palatal swellings, but they may rarely be accompanied by pain and/or purulent discharge. The cysts are generally treated by .

The diagnosis can be made prenatally; routine obstetric ultrasound can identify the characteristic hypoechoic lesion inferior and medial to the globe. It is important to distinguish a dacrocystocele from the more serious encephalocele, which is a neural tube defect.

A dacryocystocele can be diagnosed postpartum with a non-invasive ultrasound (US).

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.

While Bartholin cysts can be quite painful, they are not life-threatening. New cysts cannot absolutely be prevented from forming, but surgical or laser removal of a cyst makes it less likely that a new one will form at the same site. Those with a cyst are more likely than those without a cyst to get one in the future. They can recur every few years or more frequently. Many women who have marsupialization done find that the recurrences may slow, but do not actually stop.

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.

Choledochal cysts are treated by surgical excision of the cyst with the formation of a roux-en-Y anastomosis hepaticojujenostomy/ choledochojujenostomy to the biliary duct.

Future complications include cholangitis and a 2% risk of malignancy, which may develop in any part of the biliary tree. A recent article published in Journal of Surgery suggested that choledochal cysts could also be treated with single-incision laparoscopic hepaticojejunostomy with comparable results and less scarring. In cases of saccular type of cyst, excision and placement of T-shaped tube is done.

Currently, there is no accepted indication for fetal intervention in the management of prenatally suspected choledochal cysts.

Pancreas divisum in individuals with no symptoms does not require treatment. Treatment of those with symptoms varies and has not been well established. A surgeon may attempt a sphincterotomy by cutting the minor papilla to enlarge the opening and allow pancreatic enzymes to flow normally. During surgery, a stent may be inserted into the duct to ensure that the duct will not close causing a blockage. This surgery can cause pancreatitis in patients, or in rare cases, kidney failure and death.

An association with adenoma of the minor papilla has been reported.

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

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.

Urethral diverticulum is often an incidental finding. It can be diagnosed using magnetic resonance imaging and/or micturating cystourethrography. Other studies that can be used to diagnose urethral diverticulum include intravenous urography, urethroscopy, and/or ultrasound. Conditions that should be distinguished from urethral diverticulum in a differential diagnosis include overactive bladder, Gartner's duct cyst, Gartner's duct abscess, ectopic caeco-ureterocele, interstitial cystitis, pelvic inflammatory disease, endometriosis, and cancer.