Cholesterol gallstone formation risk factors include age, female sex, family history, race, pregnancy, parity, obesity, birth control, diabetes mellitus, cirrhosis, prolonged fasting, rapid weight loss, total parenteral nutrition, ileal disease and impaired gallbladder emptying.

Patients that have gallstones and biliary colic are at increased risk for complications, including cholecystitis. Complications from gallstone disease is 0.3% per year and therefore prophylactic cholecystectomy are rarely indicated unless part of a special population that includes porcelain gallbladder, individuals eligible for organ transplant, diabetics and those with sickle cell anemia.

The presence of gallstones can lead to inflammation of the gall bladder (cholecystitis) or the biliary tree (cholangitis) or acute inflammation of the pancreas (pancreatitis). Rarely, a gallstone can become impacted in the ileocecal valve that joins the caecum and the ileum, causing gallstone ileus (mechanical ileus).

Complications from delayed surgery include pancreatitis, empyema, and perforation of the gallbladder, cholecystitis, cholangitis, and obstructive jaundice.

Biliary pain in the absence of gallstones, known as postcholecystectomy syndrome, may severely impact the patient's quality of life, even in the absence of disease progression.

Possible causes:

- pregnancy

- androgens

- birth control pills

- antibiotics (such as TMP/SMX)

- abdominal mass (e.g. cancer)

- biliary atresia and other pediatric liver diseases

- biliary trauma

- congenital anomalies of the biliary tract

- gallstones

- acute hepatitis

- cystic fibrosis

- intrahepatic cholestasis of pregnancy (obstetric cholestasis)

- primary biliary cirrhosis, an autoimmune disorder

- primary sclerosing cholangitis, associated with inflammatory bowel disease

- some drugs (e.g. flucloxacillin and erythromycin)

Drugs such as gold salts, nitrofurantoin, anabolic steroids, chlorpromazine, prochlorperazine, sulindac, cimetidine, erythromycin, estrogen, and statins can cause cholestasis and may result in damage to the liver.

Extrahepatic cholestasis can usually be treated by surgery.

Pruritis in cholestatic jaundice is treated by Antihistamines, Ursodeoxycholic Acid, Phenobarbital

The cancer commonly spreads to the liver, bile duct, stomach, and duodenum.

Most tumors are adenocarcinomas, with a small percent being squamous cell carcinomas.

- Rare tumor, the U.S. incidence is 3 cases per 100,000 people each year

- Gallbladder cancer is more common in South American countries, Japan, and Israel. In Chile gallbladder cancer is the fourth most common cause of cancer deaths.

- 5th most common gastrointestinal cancer

- Up to 5 times more common in women than men depending on population (e.g. 73% female in China ).

- The age adjusted incidence rates of gall bladder cancer is highest in Chile followed by In the state of Assam in India

Black pigment gallstones can form in Rokitansky–Aschoff sinuses of the gallbladder after the fourth to fifth decades of life in absence of the typical risk factors for bilirubin suprasaturation of bile. Hence, they are associated with gallstones (cholelithiasis). Cases of gall bladder cancer have also been reported to arise from Rokitansky–Aschoff sinuses.

Alcohol has been suggested as a risk factor for gall bladder cancer. Evidence suggests that a high intake of alcohol is associated with gall bladder cancer. Men may be at a higher risk of alcohol-related gallbladder cancer than women.

Drinking may be a cause of earlier onset of colorectal cancer. The evidence that alcohol is a cause of bowel cancer is convincing in men and probable in women.

The National Institutes of Health, the National Cancer Institute, Cancer Research, the American Cancer Society, the Mayo Clinic, and the Colorectal Cancer Coalition, American Society of Clinical Oncology and the Memorial Sloan-Kettering Cancer Center list alcohol as a risk factor.

A WCRF panel report finds the evidence "convincing" that alcoholic drinks increase the risk of colorectal cancer in men at consumption levels above 30 grams of absolute alcohol daily. The National Cancer Institute states, "Heavy alcohol use may also increase the risk of colorectal cancer"

A 2011 meta-analysis found that alcohol consumption was associated with an increased risk of colorectal cancer.

Sphincter of Oddi dysfunction may be suggested by pain which seems to come from a biliary origin, which may or may not be associated with transient increases of liver or pancreatic enzymes. Common bile duct dilation and episodes of pancreatitis are also signs.

Sphincter of Oddi dysfunction refers to a group of functional disorders leading to abdominal pain due to dysfunction of the Sphincter of Oddi: functional biliary sphincter of Oddi and functional pancreatic sphincter of Oddi disorder. The sphincter of Oddi is a sphincter muscle, a circular band of muscle at the bottom of the biliary tree which controls the flow of pancreatic juices and bile into the second part of the duodenum. The pathogenesis of this condition is recognized to encompass stenosis or dyskinesia of the sphincter of Oddi (especially after cholecystectomy); consequently the terms biliary dyskinesia, papillary stenosis, and postcholecystectomy syndrome have all been used to describe this condition. Both stenosis and dyskinesia can obstruct flow through the sphincter of Oddi and can therefore cause retention of bile in the biliary tree and pancreatic juice in the pancreatic duct.

Individuals with sphincter of Oddi dysfunction present with abdominal pain resembling that of structural or inflammatory disorders of the gallbladder, biliary tree or pancreas. Among other characteristics, the pain is typically in the upper part of the abdomen or in the right upper quadrant of the abdomen, lasts 30 minutes or longer, and is not associated with a structural abnormality that could lead to these symptoms. The disorder is classified into two subtypes: functional biliary sphincter of Oddi disorder, where there is no disturbance in pancreatic enzyme measurements, such as amylase and lipase; and, functional pancreatic sphincter of Oddi disorder, where pancreatic enzyme measurements are elevated.

Attacks can be precipitated by opioid analgesics, particularly in patients having undergone cholecystectomy (gall bladder removal) or who have had bariatric surgery (Gastric Bypass or weight loss surgery).

They form as a result of increased pressure in the gallbladder and recurrent damage to the wall of the gallbladder.

Biliary injury (bile duct injury) is the traumatic damage of the bile ducts. It is most commonly an iatrogenic complication of cholecystectomy — surgical removal of gall bladder, but can also be caused by other operations or by major trauma. The risk of biliary injury is more during laparoscopic cholecystectomy than during open cholecystectomy. Biliary injury may lead to several complications and may even cause death if not diagnosed in time and managed properly. Ideally biliary injury should be managed at a center with facilities and expertise in endoscopy, radiology and surgery.

The cancerous mass tends to block food from getting to the small intestine. If food cannot get to the intestines, it will cause pain, acid reflux, and weight loss because the food cannot get to where it is supposed to be processed and absorbed by the body.

Patients with duodenal cancer may experience abdominal pain, weight loss, nausea, vomiting, and chronic GI bleeding.

Many causes exist including:

- diverticulitis : most common ~ 60%

- colorectal cancer (CRC) : ~ 20%

- Crohn's disease : ~ 10%

- radiotherapy

- appendicitis

- trauma

Equine enteroliths are found by walking pastures or turning over manure compost piles to find small enteroliths, during necroscopy, and increasingly, during surgery for colic. Therefore, the incidence of asymptomatic enteroliths is unknown.

Equine enteroliths typically are smoothly spherical or tetrahedral, consist mostly of the mineral struvite (ammonium magnesium phosphate), and have concentric rings of mineral precipitated around a nidus.

Enteroliths in horses were reported widely in the 19th century, infrequently in the early 20th century, and now increasingly. They have also been reported in zebras: five in a zoo in California and one in a zoo in Wisconsin. Struvite enteroliths are associated with elevated pH and mineral concentrations in the lumen. In California, struvite enteroliths are associated also with a high proportion of alfalfa in the feed and less access to grass pasture. This association has been attributed to the cultivation of alfalfa on serpentine soils, resulting in high concentrations of magnesium in the alfalfa.

Stones can cause disease by several mechanisms:

- Irritation of nearby tissues, causing pain, swelling, and inflammation

- Obstruction of an opening or duct, interfering with normal flow and disrupting the function of the organ in question

- Predisposition to infection (often due to disruption of normal flow)

A number of important medical conditions are caused by stones:

- Nephrolithiasis (kidney stones)

- Can cause hydronephrosis (swollen kidneys) and renal failure

- Can predispose to pyelonephritis (kidney infections)

- Can progress to urolithiasis

- Urolithiasis (urinary bladder stones)

- Can progress to bladder outlet obstruction

- Cholelithiasis (gallstones)

- Can predispose to cholecystitis (gall bladder infections) and ascending cholangitis (biliary tree infection)

- Can progress to choledocholithiasis (gallstones in the bile duct) and gallstone pancreatitis (inflammation of the pancreas)

- Gastric calculi can cause colic, obstruction, torsion, and necrosis.

In humans, enteroliths are rare and may be difficult to distinguish from gall stones. Their chemical composition is diverse, and rarely can a nidus be found. A differential diagnosis of an enterolith requires the enterolith, a normal gallbladder, and a diverticulum.

An enterolith typically forms within a diverticulum. An enterolith formed in a Meckel's diverticulum sometimes is known as a Meckel's enterolith. Improper use of magnesium oxide as a "long-term" laxative has been reported to cause enteroliths and/or medication bezoars.

Most enteroliths are not apparent and cause no complications. However, any complications that do occur are likely to be severe. Of these, bowel obstruction is most common, followed by ileus and perforation. Bowel obstruction and ileus typically occur when a large enterolith is expelled from a diverticulum into the lumen. Perforation typically occurs within the diverticulum.

Most human enteroliths are radiolucent on plain X-rays. They sometimes can be visualized on CT scans without contrast; presence of contrast in the lumen may reveal the enterolith as a void. Most often, they are visualized using ultrasound.

Although recent surveys of enterolith composition are lacking, one early review notes struvite (as in equines), calcium phosphate, and calcium carbonate and reports choleic acid. Deoxycholic acid and cholic acid have also been reported.

Urethral diverticulum can occur in men, and can cause complications including kidney stones and urinary tract infections.

Resection is sometimes a part of a treatment plan, but duodenal cancer is difficult to remove surgically because of the area that it resides in—there are many blood vessels supplying the lower body. Chemotherapy is sometimes used to try to shrink the cancerous mass. Other times intestinal bypass surgery is tried to reroute the stomach to intestine connection around the blockage.

A 'Whipple' procedure is a type of surgery that is sometimes possible with this cancer. In this procedure, the duodenum, a portion of the Pancreas (the head), and the gall bladder are usually removed, the small intestine is brought up to the Pylorus (the valve at the bottom of the stomach) and the Liver and Pancreas digestive enzymes and bile are connected to the small intestine below the Pylorus.

The removal of part of the Pancreas often requires taking Pancreatic Enzyme supplements to aid digestion. These are available in the form of capsules by prescription.

It is not unusual for a patient having received a Whipple procedure to feel perfectly well, and to lead his/her normal life without difficulty.

It is important for the procedure to be performed by a surgeon with extensive experience having done and observed the procedure, as specific competence makes a big difference.

Some patients need to be fitted with tubes to either add nutrients (feeding tubes) or drainage tubes to remove excess processed food that can not pass the blockage.

The incidence of urethral diverticulum has been increasing in the 2000s, likely due to increasing diagnosis and detection of the condition. It is estimated to be present in as low as 0.02% of all women and as high as 6% of all women, and 40% of women with lower urinary tract symptoms. Most symptomatic urethral diverticula are present in women from 30–60 years old.

84% of periurethral masses are due to urethral diverticula.

A fistula involving the bladder can have one of many specific names, describing the specific location of its outlet:

- Bladder and intestine: "vesicoenteric", "enterovesical", or "vesicointestinal"

- Bladder and colon: "vesicocolic" or "colovesical"

- Bladder and rectum: "vesicorectal" or "rectovesical"

Cancer of the stomach, also called gastric cancer, is the fourth-most-common type of cancer and the second-highest cause of cancer death globally. Eastern Asia (China, Japan, Korea, Mongolia) is a high-risk area for gastric cancer, and North America, Australia, New Zealand and western and northern Africa are areas with low risk. The most common type of gastric cancer is adenocarcinoma, which causes about 750,000 deaths each year. Important factors that may contribute to the development of gastric cancer include diet, smoking and alcohol consumption, genetic aspects (including a number of heritable syndromes) and infections (for example, "Helicobacter pylori" or Epstein-Barr virus) and pernicious anemia. Chemotherapy improves survival compared to best supportive care, however the optimal regimen is unclear.

In kidney stones, calcium oxalate is the most common mineral type (see Nephrolithiasis). Uric acid is the second most common mineral type, but an "in vitro" study showed uric acid stones and crystals can promote the formation of calcium oxalate stones.

Esophageal cancer is the sixth-most-common cancer in the world, and its incidence is increasing. Some three to five males are affected for each female. An "esophageal cancer belt", in which the incidence of esophageal squamous cell carcinoma (SCC) is more than a hundred times that of adjacent areas, extends from northeastern China through central Asia to northern Iran. Ethiopia also has a notably high incidence. There are two main types of esophageal cancer—adenocarcinoma and squamous cell carcinoma. Worldwide, the incidence of each type is about the same, but in developed countries like North America and Europe adenocarcinoma is the more common.

Cancer of the esophagus is often detected late inasmuch as there are typically no early symptoms. Nevertheless, if the cancer is caught soon enough, patients can have a five-year survival rate of 90% or above. By the time esophageal cancer is usually detected, though, it might have spread beyond the esophageal wall, and the survival rate drops significantly. In China, the overall five-year survival rate for advanced esophageal cancer is about 20%, and in the United States it is about 15%.