Symptoms depend on the location of the duplication. Duplications occurring high in the gastrointestinal tract (e.g. esophageal) may cause difficulty breathing due to compression of the airway. Lower gastrointestinal duplications (e.g. duodenum, colon) can be associated with abdominal pain, gastrointestinal bleeding, a palpable mass, vomiting, or may cause bowel obstruction. Smaller lesions can act as a so-called "lead point" for intussusception.

Duplications are usually removed surgically, even if they are found incidentally (i.e. not causing symptoms or encountered on routine studies for other reasons), as there is a high incidence of complications resulting from untreated cases. Cysts are often technically easier to remove than tubular malformations since tubular structures usually share a blood supply with the associated gut.

Prenatally diagnosed hydronephrosis (fluid-filled kidneys) suggest post-natal follow-up examination.

The strongest neo-natal presentation is urinary tract infection. A hydronephrotic kidney may present as a palpable abdominal mass in the newborn, and may suggest an ectopic ureter or ureterocele.

In older children, ureteral duplication may present as:

- Urinary tract infection - most commonly due to vesicoureteral reflux (flow of urine from the bladder into the ureter, rather than vice versa).

- Urinary incontinence in females occurs in cases of ectopic ureter entering the vagina, urethra or vestibule.

Medullary sponge kidney (also known as Cacchi–Ricci disease) is a congenital disorder of the kidneys characterized by cystic dilatation of the collecting tubules in one or both kidneys. Individuals with medullary sponge kidney are at increased risk for kidney stones and urinary tract infection (UTI). Patients with MSK typically pass twice as many stones per year as do other stone formers without MSK. While described as a "benign" disorder with a low morbidity rate, as many as 10% of patients with MSK have an increased risk of morbidity associated with frequent stones and UTIs. While some patients report increased chronic kidney pain, the source of the pain, when a UTI or blockage is not present, is unclear at this time. Renal colic (flank and back pain) is present in 55% of patients. Women with MSK experience more stones, UTIs, and complications than men. MSK was previously believed not to be hereditary but there is more evidence coming forth that may indicate otherwise.

Most cases are asymptomatic or are discovered during an investigation of blood in the urine. Symptomatic patients typically present as middle-aged adults with renal colic, kidney stones, nephrocalcinosis and/or recurrent urinary tract infections; however, MSK also may affect children very rarely. In addition to the typical clinical phenotype of recurrent stone disease, other clinical profiles have now been recognized, that is, an indolent, almost asymptomatic MSK, and a rare form characterized by intractable pain.

Duplicated ureter or Duplex Collecting System is a congenital condition in which the ureteric bud, the embryological origin of the ureter, splits (or arises twice), resulting in two ureters draining a single kidney. It is the most common renal abnormality, occurring in approximately 1% of the population. The additional ureter may result in a ureterocele, or an ectopic ureter.

Not all patients with Schatzki rings have symptoms; barium swallow tests of the esophagus sometimes show Schatzki rings in patients with no swallowing difficulties.

When Schatzki rings cause symptoms, they usually result in episodic difficulties with swallowing (dysphagia) solid foods, or a sensation that the food "sticks" while swallowing, especially if the food is not chewed thoroughly. Patients usually are able to regurgitate or force through the food material and resume eating. However, complete obstruction of the esophagus by a bolus of food (often called steakhouse syndrome) can occur. This can cause crushing chest pain and may need immediate treatment with endoscopy, which is the use of a specialized fibre-optic camera in order to remove the lodged food. After the obstruction is located, snares or forceps are inserted to pull the food out of the esophagus or to push it into the stomach. The latter is done with caution, usually when the anatomy of the structures around the obstruction is already known.

A Schatzki ring or Schatzki–Gary ring is a narrowing of the lower esophagus that can cause difficulty swallowing (dysphagia). The narrowing is caused by a ring of mucosal tissue (which lines the esophagus) or muscular tissue. A Schatzki ring is a specific type of "esophageal ring", and Schatzki rings are further subdivided into those above the esophagus/stomach junction (A rings), and those found at the squamocolumnar junction in the lower esophagus (B rings).

Patients with Schatzki rings can develop intermittent difficulty swallowing or, more seriously, a completely blocked esophagus. The ring is named after the German-American physician Richard Schatzki.

Atresia is a condition in which an orifice or passage in the body is (usually abnormally) closed or absent.

Examples of atresia include:

- Biliary atresia, a condition in newborns in which the common bile duct between the liver and the small intestine is blocked or absent.

- Choanal atresia, blockage of the back of the nasal passage, usually by abnormal bony or soft tissue.

- Esophageal atresia, which affects the alimentary tract and causes the esophagus to end before connecting normally to the stomach.

- Imperforate anus, malformation of the opening between the rectum and anus.

- Intestinal atresia, malformation of the intestine, usually resulting from a vascular accident in utero.

- Microtia, absence of the ear canal or failure of the canal to be tubular or fully formed (can be related to Microtia, a congenital deformity of the pinna, or outer ear).

- Ovarian follicle atresia, the degeneration and subsequent resorption of one or more immature ovarian follicles.

- Potter sequence, congenital decreased size of the kidney leading to absolutely no functionality of the kidney, usually related to a single kidney.

- Pulmonary atresia, malformation of the pulmonary valve in which the valve orifice fails to develop.

- Renal agenesis, only having one kidney.

- Tricuspid atresia, a form of congenital heart disease whereby there is a complete absence of the tricuspid valve, and consequently an absence of the right atrioventricular connection.

- Vaginal atresia, a congenital occlusion of the vagina or subsequent adhesion of the walls of the vagina, resulting in its occlusion.

Esophageal diseases can derive from congenital conditions, or they can be acquired later in life.

Many people experience a burning sensation in their chest occasionally, caused by stomach acids refluxing into the esophagus, normally called heartburn. Extended exposure to heartburn may erode the lining of the esophagus, leading potentially to Barrett's esophagus which is associated with an increased risk of adenocarcinoma most commonly found in the distal one-third of the esophagus.

Some people also experience a sensation known as globus esophagus, where it feels as if a ball is lodged in the lower part of the esophagus.

The following are additional diseases and conditions that affect the esophagus:

- Achalasia

- Acute esophageal necrosis

- Barrett's esophagus

- Boerhaave syndrome

- Caustic injury to the esophagus

- Chagas disease

- Diffuse esophageal spasm

- Esophageal atresia and Tracheoesophageal fistula

- Esophageal cancer

- Esophageal dysphagia

- Esophageal varices

- Esophageal web

- Esophagitis

- GERD

- Hiatus hernia

- Jackhammer esophagus (hypercontractile peristalsis)

- Killian–Jamieson diverticulum

- Mallory-Weiss syndrome

- Neurogenic dysphagia

- Nutcracker esophagus

- Schatzki's ring

- Zenker's Diverticulum

Other birth defects may co-exist, particularly in the heart, but sometimes also in the anus, spinal column, or kidneys. This is known as VACTERL association because of the involvement of Vertebral column, Anorectal, Cardiac, Tracheal, Esophageal, Renal, and Limbs. It is associated with polyhydramnios in the third trimester.

This birth defect arises in the fourth fetal week, when the trachea and esophagus should begin to separate from each other.

It can be associated with disorders of the tracheoesophageal septum.

Its main symptoms are pain and difficulty in swallowing (dysphagia).

Esophageal webs are thin (2-3mm) membranes of normal esophageal tissue consisting of mucosa and submucosa that can partially protrude/obstruct the esophagus. They can be congenital or acquired. Congenital webs commonly appear in the middle and inferior third of the esophagus, and they are more likely to be circumferential with a central or eccentric orifice. Acquired webs are much more common than congenital webs and typically appear in the cervical area (postcricoid).

Clinical symptoms of this condition are selective (solid more than liquids) dysphagia, thoracic pain, nasopharyngeal reflux, aspiration, perforation and food impaction (the last two are very rare).

Esophageal stricture, or narrowing of the esophagus, is usually a complication of acid reflux, most commonly due to gastroesophageal reflux (GERD). These patients are usually older and have had GERD for a long time. Esophageal stricture can also be due to other causes, such as acid reflux from Zollinger-Ellison syndrome, trauma from a nasogastric tube placement, and chronic acid exposure in patients with poor esophageal motility from scleroderma. Other non-acid related causes of peptic strictures include infectious esophagitis, ingestion of chemical irritant, pill irritation, and radiation. Peptic stricture is a progressive mechanical dysphagia, meaning patients will complain of initial intolerance to solids followed by inability to tolerate liquids. When the diameter of the stricture is less than 12 mm the patient will always have dysphagia, while dysphagia is not seen when the diameter of the stricture is above 30 mm. Symptoms relating to the underlying cause of the stricture usually will also be present.

Esophageal cancer also presents with progressive mechanical dysphagia. Patients usually come with

rapidly progressive dysphagia first with solids then with liquids, weight loss (> 10 kg), and anorexia (loss of appetite). Esophageal cancer usually affects the elderly. Esophageal cancers can be either squamous cell carcinoma or adenocarcinoma. Adenocarcinoma is the most prevalent in the US and is associated with patients with chronic GERD who have developed Barrett's esophagus (intestinal metaplasia of esophageal mucosa). Squamous cell carcinoma is more prevalent in Asia and is associated with tobacco smoking and alcohol use.

Esophageal rings and webs, are actual rings and webs of tissue that may occlude the esophageal lumen.

- "Rings" --- Also known as Schatzki rings from the discoverer, these rings are usually mucosal rings rather than muscular rings, and are located near the gastroesophageal junction at the squamo-columnar junction. Presence of multiple rings may suggest eosinophilic esophagitis. Rings cause intermittent mechanical dysphagia, meaning patients will usually present with transient discomfort and regurgitation while swallowing solids and then liquids, depending on the constriction of the ring.

- "Webs" --- Usually squamous mucosal protrusion into the esophageal lumen, especially anterior cervical esophagus behind the cricoid area. Patients are usually asymptomatic or have intermittent dysphagia. An important association of esophageal webs is to the Plummer-Vinson syndrome in iron deficiency, in which case patients will also have anemia, koilonychia, fatigue, and other symptoms of anemia.

Achalasia is an idiopathic motility disorder characterized by failure of lower esophageal sphincter (LES) relaxation as well as loss of peristalsis in the distal esophagus, which is mostly smooth muscle. Both of these features impair the ability of the esophagus to empty contents into the stomach. Patients usually complain of dysphagia to both solids and liquids. Dysphagia to liquids, in particular, is a characteristic of achalasia. Other symptoms of achalasia include regurgitation, night coughing, chest pain, weight loss, and heartburn. The combination of achalasia, adrenal insufficiency, and alacrima (lack of tear production) in children is known as the triple A (Allgrove) syndrome. In most cases the cause is unknown (idiopathic), but in some regions of the world, achalasia can also be caused by Chagas disease due to infection by "Trypanosoma cruzi".

Scleroderma is a disease characterized by atrophy and sclerosis of the gut wall, most commonly of the distal esophagus (~90%). Consequently, the lower esophageal sphincter cannot close and this can lead to severe gastroesophageal reflux disease (GERD). Patients typically present with progressive dysphagia to both solids and liquids secondary to motility problems or peptic stricture from acid reflux.

Spastic motility disorders include diffuse esophageal spasm (DES), nutcracker esophagus, hypertensive lower esophageal sphincter, and nonspecific spastic esophageal motility disorders (NEMD).

- "DES" can be caused by many factors that affect muscular or neural functions, including acid reflux, stress, hot or cold food, or carbonated drinks. Patients present with intermittent dysphagia, chest pain, or heartburn.

Rare causes of esophageal dysphagia not mentioned above

- Diverticulum

- Aberrant subclavian artery, or (dysphagia lusoria)

- Cervical osteophytes

- Enlarged aorta

- Enlarged left atrium

- Mediastinal tumor

The three most common symptoms of Opitz G/BBB syndrome (both type I & II) are hypertelorism (exceptionally wide-spaced eyes), laryngo-tracheo-esophalgeal defects (including clefts and holes in the palate, larynx, trachea and esophagus) and hypospadias (urinary openings in males not at the tip of the penis) (Meroni, Opitz G/BBB syndrome, 2012). Abnormalities in the larynx, trachea and esophagus can cause significant difficulty breathing and/or swallowing and can result in reoccurring pneumonia and life-threatening situations. Commonly, there may be a gap between the trachea and esophagus, referred to as a laryngeal cleft; which can allow food or fluid to enter the airway and make breathing and eating a difficult task.

Genital abnormalities like a urinary opening under the penis (hypospadias), undescended testes (cryptorchidism), underdeveloped scrotum and a scrotum divided into two lobes (bifid scrotum) can all be commonplace for males with the disease.

Developmental delays of the brain and nervous system are also common in both types I and II of the disease. 50% of people with Opitz G/BBB Syndrome will experience developmental delay and mild intellectual disability. This can impact motor skills, speech and learning capabilities. Some of these instances are likened to autistic spectrum disorders. Close to half of the people with Opitz G/BBB Syndrome also have a cleft lip (hole in the lip opening) and possibly a cleft palate (hole in the roof of the mouth), as well. Less than half of the people diagnosed have heart defects, imperforate anus (obstructed anal opening), and brain defects. Of all the impairments, female carriers of X-linked Type I Opitz G/BBB Syndrome usually only have ocular hypertelorism.

Nutcracker esophagus is characterized as a motility disorder of the esophagus, meaning that it is caused by abnormal movement, or peristalsis of the esophagus. Patients with motility disorders present with two key symptoms: either with chest pain (typically reported as non-cardiac chest pain as it is esophageal in origin), which is usually found in disorders of spasm, or with dysphagia (difficulty with swallowing). Nutcracker esophagus can present with either of these, but chest pain is the more common presentation. The chest pain is very severe and intense, and mimics cardiac chest pain. It may spread into the arm and back. The symptoms of nutcracker esophagus are intermittent, and may occur with or without food. Rarely, patients can present with a sudden obstruction of the esophagus after eating food (termed a food bolus obstruction, or the 'steakhouse syndrome') requiring urgent treatment. The disorder does not progress to produce worsening symptoms or complications, unlike other motility disorders (such as achalasia) or anatomical abnormalities of the esophagus (such as peptic strictures or esophageal cancer). Many patients with nutcracker esophagus do not have any symptoms at all, as esophageal manometry studies done on patients without symptoms may show the same motility findings as nutcracker esophagus. Nutcracker esophagus may also be associated with metabolic syndrome. The incidence of nutcracker esophagus in all patients is uncertain.

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

Patients usually complain of dysphagia (the feeling of food getting stuck "several seconds" after swallowing), and will point to the suprasternal notch or behind the sternum as the site of obstruction.

X-linked type I Opitz G/BBB Syndrome is diagnosed on clinical findings, but those findings can vary greatly: even within the same family. Manifestations of X-linked type I are classified in the frequent/major findings and minor findings that are found in less than 50% of individuals.

The three major findings that suggest a person has X-linked Type I Opitz G/BBB Syndrome:

1. Ocular hypertelorism (~100% cases)

2. Hypospadias (85-90% cases)

3. Laryngotracheoesophageal abnormalities (60-70%)

Minor findings found in less than 50% of individuals:

1. Developmental delay (especially intellectually)

2. Cleft lip/palate

3. Congenital heart defects

4. Imperforate (blocked) anus

5. Brain defects (especially corpus callosum)

In 1989, Hogdall used ultrasonographs to diagnose X-linked Type I Opitz G/BBB Syndrome after 19 weeks of pregnancy, by identifying hypertelorism (widely-spaced eyes) and hypospadias (irregular urinary tract openings in the penis).

There is also molecular genetic testing available to identify mutations leading to Opitz G/BBB Syndrome. X-linked Type I testing must be done on MID1, since this is the only gene that is known to cause Type I Opitz G/BBB Syndrome. Two different tests can be performed: sequence analysis and deletion/duplication analysis. In the sequence analysis a positive result would detect 15-50% of the DNA sequence mutated, while a deletion/duplication positive result would find deletion or duplication of one or more exons of the entire MID1 gene.

The change from normal to premalignant cells that indicate Barrett's esophagus does not cause any particular symptoms. Barrett's esophagus, however, is associated with these symptoms:

- frequent and longstanding heartburn

- trouble swallowing (dysphagia)

- vomiting blood (hematemesis)

- pain under the sternum where the esophagus meets the stomach

- unintentional weight loss because eating is painful (odynophagia)

The risk of developing Barrett's esophagus is increased by central obesity (vs. peripheral obesity). The exact mechanism is unclear. The difference in distribution of fat among men (more central) and women (more peripheral) may explain the increased risk in males.

Esophageal webs are thin membranes occurring anywhere along the esophagus.

The most common symptoms of GERD in adults are an acidic taste in the mouth, regurgitation, and heartburn. Less common symptoms include pain with swallowing/sore throat, increased salivation (also known as water brash), nausea, chest pain, and coughing.

GERD sometimes causes injury of the esophagus. These injuries may include one or more of the following:

- Reflux esophagitis – inflammation of esophageal epithelium which can cause ulcers near the junction of the stomach and esophagus

- Esophageal strictures – the persistent narrowing of the esophagus caused by reflux-induced inflammation

- Barrett's esophagus – intestinal metaplasia (changes of the epithelial cells from squamous to intestinal columnar epithelium) of the distal esophagus

- Esophageal adenocarcinoma – a form of cancer

Some researchers have proposed that recurrent ear infections, and idiopathic pulmonary fibrosis might be tied, in some cases, to GERD; however, a causative role has not been established. GERD does not appear to be linked to chronic sinusitis.

Barrett's esophagus refers to an abnormal change (metaplasia) in the cells of the lower portion of the esophagus. It is characterized by the replacement of the normal stratified squamous epithelium lining of the esophagus by simple columnar epithelium with goblet cells (which are usually found lower in the gastrointestinal tract). The medical significance of Barrett's esophagus is its strong association (0.1 per 1 cm Prague C>M> total segment length per patient-year) with esophageal adenocarcinoma, a very often deadly cancer, because of which it is considered to be a premalignant condition.

The main cause of Barrett's esophagus is thought to be an adaptation to chronic acid exposure from reflux esophagitis. The incidence of esophageal adenocarcinoma has increased substantially in the Western world in recent years. The condition is found in 5–15% of patients who seek medical care for heartburn (gastroesophageal reflux disease), although a large subgroup of patients with Barrett's esophagus do not have symptoms. Diagnosis requires endoscopy (more specifically, esophagogastroduodenoscopy, a procedure in which a fibreoptic cable is inserted through the mouth to examine the esophagus, stomach, and duodenum) and biopsy. The cells of Barrett's esophagus, after biopsy, are classified into four general categories: nondysplastic, low-grade dysplasia, high-grade dysplasia, and frank carcinoma. High-grade dysplasia and early stages of adenocarcinoma can be treated by endoscopic resection and new endoscopic therapies such as radiofrequency ablation, whereas advanced stages (submucosal) are generally advised to undergo surgical treatment. Nondysplastic and low-grade patients are generally advised to undergo annual observation with endoscopy, with radiofrequency ablation as a therapeutic option. In high-grade dysplasia, the risk of developing cancer might be at 10% per patient-year or greater.

The condition is named after the Australian-born British thoracic surgeon Norman Barrett (1903–1979), who described it in 1950.

Those with the eating disorder bulimia are more likely to develop Barrett’s esophagus because bulimia can cause severe acid reflux, and because purging also floods the esophagus with acid.

Nephrogenic adenoma, also mesonephric adenoma and nephrogenic metaplasia, is a benign growth typically found in the urinary bladder.

It is thought to result from displacement and implantation of renal tubular cells, as this entity in kidney transplant recipients has been shown to be kidney donor derived.

This entity should not be confused with the similar-sounding "metanephric adenoma".

A Killian–Jamieson diverticulum is an outpouching of the esophagus just below the upper esophageal sphincter.

The physicians that first discovered the diverticulum were Gustav Killian and James Jamieson. Diverticula are seldom larger than 1.5 cm, and are less frequent than the similar Zenker's diverticula. As opposed to a Zenker's, which is typically a posterior and inferior outpouching from the esophagus, a Killian–Jamieson diverticulum is typically an anterolateral outpouching at the level of the C5-C6 vertebral bodies, due to a congenital weakness in the cervical esophagus just below the cricopharyngeal muscle. It is usually smaller in size than a Zenker's diverticulum, and typically asymptomatic. Although congenital, it is more commonly seen in elderly patients.