Primary sclerosing cholangitis is typically classified into three subgroups based on whether the small and/or large bile ducts are affected. The subgroups of PSC include the following:

- Classic PSC

- Small-duct PSC

- PSC associated with autoimmune hepatitis

The first symptoms typically include fever, intermittent abdominal pain, and hepatomegaly. Occasionally, jaundice occurs.

Morbidity is common and is caused by complications of cholangitis, sepsis, choledocholithiasis, and cholangiocarcinoma. These morbid conditions often prompt the diagnosis. Portal hypertension may be present, resulting in other conditions including splenomegaly, hematemesis, and melena. These problems can severely affect the patient's quality of life. In a 10-year period between 1995 and 2005, only 10 patients were surgically treated for Caroli disease, with an average patient age of 45.8 years.

After reviewing 46 cases of Caroli disease before 1990, 21.7% of the cases were the result of an intraheptic cyst or nonobstructive biliary tree dilation, 34.7% were linked with congenital hepatic fibrosis, 13% were isolated choledochal cystic dilation, and the remaining 24.6% had a combination of all three.

Nearly half of people with PSC do not have symptoms and are often incidentally discovered to have PSC due to abnormal liver function tests, but a substantial proportion will have debilitating signs and symptoms of the disease. Signs and symptoms of PSC may include severe itching and non-specific fatigue. Yellowing of the skin and white portion of the eyes may also be seen. Enlargement of the liver and spleen are seen in approximately 40% of affected individuals. Abdominal pain affects about 20% of people with PSC.

Multiple episodes of life-threatening acute cholangitis (infection within the bile ducts) can be seen due to impaired drainage of the bile ducts, which increases the risk of infection.

- Dark urine due to excess conjugated bilirubin, which is water-soluble and excreted by the kidneys (i.e. choluria)

- Malabsorption, especially of fat, and steatorrhea (fatty stool), due to an inadequate amount of bile reaching the small intestine, leading to decreased levels of the fat-soluble vitamins, A, D, E and K.

- Portal hypertension, a complication of cirrhosis, which can manifest with esophageal and parastomal varices as well as hepatic encephalopathy (mental status alteration/disturbance caused by liver dysfunction and shunting of blood away from the scarred liver; such that ammonia detoxification is reduced with concomitant encephalopathy).

At CT scans, bile duct hamartomas appear as small, well-defined hypo- or isoattenuating masses with little or no enhancement after contrast administration. At MRI, they appear hypointense on T1-weighted images, iso- or slightly hyperintense on T2-weighted images, and hypointense after administration of gadolinium based contrast-agent. On imaging, multiple hamartomas may look similar to metastases or microabscesses.

Murphy's sign is commonly negative on physical examination in choledocholithiasis, helping to distinguish it from cholecystitis. Jaundice of the skin or eyes is an important physical finding in biliary obstruction. Jaundice and/or clay-colored stool may raise suspicion of choledocholithiasis or even gallstone pancreatitis. If the above symptoms coincide with fever and chills, the diagnosis of ascending cholangitis may also be considered.

Greater than 70% of people with gallstones are asymptomatic and are found incidentally on ultrasound. Studies have shown that 10% of those people will develop symptoms within five years of diagnosis and 20% within 20 years.

Initially, the symptoms of biliary atresia are indistinguishable from those of neonatal jaundice, a usually harmless condition commonly seen in infants. Distinctive symptoms of biliary atresia are usually evident between one and six weeks after birth. Infants and children with biliary atresia develop progressive cholestasis, a condition in which bile is unable to leave the liver and builds up inside of it. When the liver is unable to excrete bilirubin through the bile ducts in the form of bile, bilirubin begins to accumulate in the blood, causing symptoms. These symptoms include yellowing of the skin, itchiness, poor absorption of nutrients (causing delays in growth), pale stools, dark urine, and a swollen abdomen. Eventually, cirrhosis with portal hypertension will develop. If left untreated, biliary atresia can lead to liver failure. Unlike other forms of jaundice, however, biliary-atresia-related cholestasis mostly does not result in kernicterus, a form of brain damage resulting from liver dysfunction. This is because in biliary atresia, the liver, although diseased, is still able to conjugate bilirubin, and conjugated bilirubin is unable to cross the blood–brain barrier.

A Klatskin tumor (or hilar cholangiocarcinoma) is a cholangiocarcinoma (cancer of the biliary tree) occurring at the confluence of the right and left hepatic bile ducts. It is named after Dr. Gerald Klatskin.

Symptoms having to do with hepatomegaly can include several, among them the individual may experience some weight loss, poor appetite and lethargy (jaundice and bruising may also be present)

Caroli disease (communicating cavernous ectasia, or congenital cystic dilatation of the intrahepatic biliary tree) is a rare inherited disorder characterized by cystic dilatation (or ectasia) of the bile ducts within the liver. There are two patterns of Caroli disease: focal or simple Caroli disease consists of abnormally widened bile ducts affecting an isolated portion of liver. The second form is more diffuse, and when associated with portal hypertension and congenital hepatic fibrosis, is often referred to as "Caroli syndrome." The underlying differences between the two types are not well understood. Caroli disease is also associated with liver failure and polycystic kidney disease. The disease affects about one in 1,000,000 people, with more reported cases of Caroli syndrome than of Caroli disease.

Caroli disease is distinct from other diseases that cause ductal dilatation caused by obstruction, in that it is not one of the many choledochal cyst derivatives.

A bile duct hamartoma or biliary hamartoma, is a benign tumour-like malformation

of the liver.

They are classically associated with polycystic liver disease, as may be seen in the context of polycystic kidney disease, and represent a malformation of the liver plate.

Common bile duct stone, also known as choledocholithiasis, is the presence of gallstones in the common bile duct (thus "" + ""). This condition causes jaundice and liver cell damage. Treatment is by cholecystectomy and ERCP.

Gallstones may be asymptomatic, even for years. These gallstones are called "silent stones" and do not require treatment. The size and number of gallstones present does not appear to influence whether people are symptomatic or asymptomatic. A characteristic symptom of gallstones is a gallstone attack, in which a person may experience colicky pain in the upper-right side of the abdomen, often accompanied by nausea and vomiting, that steadily increases for approximately 30 minutes to several hours. A person may also experience referred pain between the shoulder blades or below the right shoulder. These symptoms may resemble those of a "kidney stone attack". Often, attacks occur after a particularly fatty meal and almost always happen at night, and after drinking.

In addition to pain, nausea, and vomiting, a person may experience a fever. If the stones block the duct and cause bilirubin to leak into the bloodstream and surrounding tissue, there may also be jaundice and itching. This can also lead to confusion. If this is the case, the liver enzymes are likely to be raised.

Embryogenically, congenital hepatic fibrosis is due to malformation of the duct plate, a round structure appearing in the eighth week of gestation that is formed by primitive hepatocytes, which differentiate into cholangiocytes. Congenital hepatic fibrosis usually presents in adolescent or young adulthood, but onset of signs and symptoms can range from early childhood through mid-life. Clinical features may vary but commonly include Cholangitis, hepatomegaly and signs of portal hypertension.

Hepatomegaly is the condition of having an enlarged liver. It is a non-specific medical sign having many causes, which can broadly be broken down into infection, hepatic tumours, or metabolic disorder. Often, hepatomegaly will present as an abdominal mass. Depending on the cause, it may sometimes present along with jaundice.

A majority of individuals born with pancreas divisum will not have symptoms. In some cases, pancreas divisum is only detected during autopsy. A small group of individuals will develop symptoms which commonly include abdominal pain, nausea, vomiting, and acute and chronic pancreatitis.

Cholestasis is a condition where bile cannot flow from the liver to the duodenum. The two basic distinctions are an obstructive type of cholestasis where there is a mechanical blockage in the duct system that can occur from a gallstone or malignancy, and metabolic types of cholestasis which are disturbances in bile formation that can occur because of genetic defects or acquired as a side effect of many medications.

A person with cholangitis may complain of abdominal pain (particularly in the right upper quadrant of the abdomen), fever, rigors (uncontrollable shaking) and a feeling of uneasiness (malaise). Some may report jaundice (yellow discoloration of the skin and the whites of the eyes).

Physical examination findings typically include jaundice and right upper quadrant tenderness. Charcot's triad is a set of three common findings in cholangitis: abdominal pain, jaundice, and fever. This was assumed in the past to be present in 50–70% of cases, although more recently the frequency has been reported as 15–20%. Reynolds' pentad includes the findings of Charcot's triad with the presence of septic shock and mental confusion. This combination of symptoms indicates worsening of the condition and the development of sepsis, and is seen less commonly still.

In the elderly, the presentation may be atypical; they may directly collapse due to sepsis without first showing typical features. Those with an indwelling stent in the bile duct (see below) may not develop jaundice.

Ductopenia refers to a reduction in the number of ducts in an organ. It is the histological hallmark of vanishing bile duct syndrome (typically <0.5 bile ducts per portal triad). The most common cause of ductopenia is primary biliary cholangitis.

Other causes of ductopenia include failing liver transplant, Hodgkin's lymphoma, graft-versus-host disease (GVHD), sarcoid, Cytomegalovirus infection, HIV and medication toxicity.

The diagnosis of SSC requires the exclusion of secondary causes of sclerosing cholangitis and recognition of associated conditions that may potentially imitate its classic cholangiographic features. It is morphologically similar to primary sclerosing cholangitis (PSC) but originates from a known pathological process. Its clinical and cholangiographic features may mimic PSC, yet its natural history may be more favorable if recognition is prompt and appropriate therapy is introduced. Sclerosing cholangitis in critically ill patients, however, is associated with rapid disease progression and poor outcome. Serologic testing, radiological imaging and histological analysis can help diagnose SSC.

Under a microscope, the individual hepatocytes will have a brownish-green stippled appearance within the cytoplasm, representing bile that cannot get out of the cell. Canalicular bile plugs between individual hepatocytes or within bile ducts may also be seen, representing bile that has been excreted from the hepatocytes but cannot go any further due to the obstruction. When these plugs occur within the bile duct, sufficient pressure (caused by bile accumulation) can cause them to rupture, spilling bile into the surrounding tissue, causing hepatic necrosis. These areas are known as bile lakes, and are typically seen only with extra-hepatic obstruction.

Mirizzi's syndrome has no consistent or unique clinical features that distinguish it from other more common forms of obstructive jaundice. Symptoms of recurrent cholangitis, jaundice, right upper quadrant pain, and elevated bilirubin and alkaline phosphatase may or may not be present. Acute presentations of the syndrome include symptoms consistent with cholecystitis.

Surgery is extremely difficult as Calot's triangle is often completely obliterated and the risks of causing injury to the CBD are high.

Gallstone disease refers to the condition where gallstones are either in the gallbladder or common bile duct. The presence of stones in the gallbladder is referred to as cholelithiasis, from the Greek "chol"- (bile) + "lith"- (stone) + -"iasis" (process). If gallstones migrate into the ducts of the biliary tract, the condition is referred to as choledocholithiasis, from the Greek "chol"- (bile) + "docho"- (duct) + "lith"- (stone) + "iasis"- (process). Choledocholithiasis is frequently associated with obstruction of the biliary tree, which in turn can lead to acute ascending cholangitis, from the Greek: "chol"- (bile) + "ang"- (vessel) + "itis"- (inflammation), a serious infection of the bile ducts. Gallstones within the ampulla of Vater can obstruct the exocrine system of the pancreas, which in turn can result in pancreatitis.

Most patients have symptoms in the first year of life. It is rare for symptoms to be undetected until adulthood, and usually adults have associated complications. The classic triad of intermittent abdominal pain, jaundice, and a right upper quadrant abdominal mass is found only in minority of patients.

In infants, choledochal cysts usually lead to obstruction of the bile ducts and retention of bile. This leads to jaundice and an enlarged liver. If the obstruction is not relieved, permanent damage may occur to the liver - scarring and cirrhosis - with the signs of portal hypertension (obstruction to the flow of blood through the liver) and ascites (fluid accumulation in the abdomen). There is an increased risk of cancer in the wall of the cyst.

In older individuals, choledochal cysts are more likely to cause abdominal pain and intermittent episodes of jaundice and occasionally cholangitis (inflammation within the bile ducts caused by the spread of bacteria from the intestine into the bile ducts). Pancreatitis also may occur. The cause of these complications may be related to either abnormal flow of bile within the ducts or the presence of gallstones

Biliary atresia, also known as extrahepatic ductopenia and progressive obliterative cholangiopathy, is a childhood disease of the liver in which one or more bile ducts are abnormally narrow, blocked, or absent. It can be congenital or acquired. As a birth defect in newborn infants, it has an incidence of one in 10,000–15,000 live births in the United States, and a prevalence of one in 16,700 in the British Isles. Biliary atresia is most common in East Asia, with a frequency of one in 5,000.

The causes of biliary atresia are not well understood. Congenital biliary atresia has been associated with certain genes, while acquired biliary atresia is thought to be a result of an autoimmune inflammatory response, possibly due to a viral infection of the liver soon after birth. The only effective treatments are surgeries such as the Kasai procedure and liver transplantation.

SSC is thought to develop as a consequence of known injuries or pathological processes of the biliary tree, such as biliary obstruction, surgical trauma to the bile duct, or ischemic injury to the biliary tree. Secondary causes of SSC include intraductal stone disease, surgical or blunt abdominal trauma, intra-arterial chemotherapy, and recurrent pancreatitis. It has been clearly demonstrated sclerosing cholangitis can develop after an episode of severe bacterial cholangitis. Also it was suggested that it can result from insult to the biliary tree by obstructive cholangitis secondary to choledocholithiasis, surgical damage, trauma, vascular insults, parasites, or congenital fibrocystic disorders. Additional causes of secondary SC are toxic, due to chemical agents or drugs.