HCC mostly occurs in people with cirrhosis of the liver, and so risk factors generally include factors which cause chronic liver disease that may lead to cirrhosis. Still, certain risk factors are much more highly associated with HCC than others. For example, while heavy alcohol consumption is estimated to cause 60-70% of cirrhosis, the vast majority of HCC occurs in cirrhosis attributed to viral hepatitis (although there may be overlap). Recognized risk factors include:

- Chronic viral hepatitis (estimated cause of 80% cases globally)

- Chronic hepatitis B (approximately 50% cases)

- Chronic hepatitis C (approximately 25% cases)

- Toxins:

- Alcohol abuse: the most common cause of cirrhosis

- Aflatoxin

- Iron overload state (Hemochromatosis)

- Metabolic:

- Nonalcoholic steatohepatitis: up to 20% progress to cirrhosis

- Type 2 diabetes (probably aided by obesity)

- Congenital disorders:

- Alpha 1-antitrypsin deficiency

- Wilson's disease (controversial; while some theorise the risk increases, case studies are rare and suggest the opposite where Wilson's disease actually may confer protection)

- Hemophilia, although statistically associated with higher risk of HCC, this is due to coincident chronic viral hepatitis infection related to repeated blood transfusions over lifetime.

The significance of these risk factors varies globally. In regions where hepatitis B infection is endemic, such as southeast China, this is the predominant cause. In populations largely protected by hepatitis B vaccination, such as the United States, HCC is most often linked to causes of cirrhosis such as chronic hepatitis C, obesity, and alcohol abuse.

Certain benign liver tumors, such as hepatocellular adenoma, may sometimes be associated with coexisting malignant HCC. There is limited evidence for the true incidence of malignancy associated with benign adenomas; however, the size of hepatic adenoma is considered to correspond to risk of malignancy and so larger tumors may be surgically removed. Certain subtypes of adenoma, particularly those with β-catenin activation mutation, are particularly associated with increased risk of HCC.

Children and adolescents are unlikely to have chronic liver disease, however, if they suffer from congenital liver disorders, this fact increases the chance of developing hepatocellular carcinoma. Specifically, children with biliary atresia, infantile cholestasis, glycogen-storage diseases, and other cirrhotic diseases of the liver are predisposed to developing HCC in childhood.

Young adults afflicted by the rare fibrolamellar variant of hepatocellular carcinoma may have none of the typical risk factors, i.e. cirrhosis and hepatitis.

The risk of hepatocellular carcinoma in type 2 diabetics is greater (from 2.5 to 7.1 times the non diabetic risk) depending on the duration of diabetes and treatment protocol. A suspected contributor to this increased risk is circulating insulin concentration such that diabetics with poor insulin control or on treatments that elevate their insulin output (both states that contribute to a higher circulating insulin concentration) show far greater risk of hepatocellular carcinoma than diabetics on treatments that reduce circulating insulin concentration. On this note, some diabetics who engage in tight insulin control (by keeping it from being elevated) show risk levels low enough to be indistinguishable from the general population. This phenomenon is thus not isolated to diabetes mellitus type 2 since poor insulin regulation is also found in other conditions such as metabolic syndrome (specifically, when evidence of non alcoholic fatty liver disease or NAFLD is present) and again there is evidence of greater risk here too. While there are claims that anabolic steroid abusers are at greater risk (theorized to be due to insulin and IGF exacerbation), the only evidence that has been confirmed is that anabolic steroid users are more likely to have hepatocellular adenomas (a benign form of HCC) transform into the more dangerous hepatocellular carcinoma.

In addition to virus-related cirrhosis described above, other causes of cirrhosis can lead to HCC. Alcohol intake correlates with risk of HCC, and the risk is far greater in individuals with an alcohol-induced cirrhotic liver. There are a few disorders that are known to cause cirrhosis and lead to cancer, including hereditary hemochromatosis and primary biliary cirrhosis.

Aflatoxin exposure can lead to the development of HCC. The aflatoxins are a group of chemicals produced by the fungi "Aspergillus flavus" (the name comes from "A. flavus" toxin) and "A. parasiticus". Food contamination by the fungi leads to ingestion of the chemicals, which are very toxic to the liver. Common foodstuffs contaminated with the toxins are cereals, peanuts and other vegetables. Contamination of food is common in Africa, South-East Asia and China. Concurrent HBV infection and aflatoxin exposure increases the risk of liver cancer to over three times that seen in HBV infected individuals without aflatoxin exposure. The mechanism by which aflatoxins cause cancer is through genetic mutation of a gene required for the prevention of cancer: p53.

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.

Alcohol is a risk factor for liver cancer, through cirrhosis. "Cirrhosis results from scar formation within the liver, most commonly due to chronic alcohol use."

"Approximately 5 percent of people with cirrhosis develop liver cancer. Cirrhosis is a disease that develops when liver cells are replaced with scar tissue after damage from alcohol abuse, …"

The NIAAA reports that "Prolonged, heavy drinking has been associated in many cases with primary liver cancer." However, it is liver cirrhosis, whether caused by alcohol or another factor, that is thought to induce the cancer."

"The chances of getting liver cancer increase markedly with five or more drinks per day" (NCI).

A study concluded that for every additional drink regularly consumed per day, the incidence of liver cancer increases by 0.7 per 1000.

In the United States, liver cancer is relatively uncommon, afflicting approximately 2 people per 100,000, but excessive alcohol consumption is linked to as many as 36% of these cases by some investigators "Overall, 61% of HCC were attributable to HCV [hepatitis C virus], 13% to HBV [hepatitis B virus], and 18% to heavy alcohol drinking." A study in the province of Brescia, northern Italy concluded, "On the basis of population attributable risks (AR), heavy alcohol intake seems to be the single most relevant cause of HCC in this area (AR: 45%), followed by HCV (AR: 36%), and HBV (AR: 22%) infection."

FHCC accounts for 1-10% of primary liver cancers. It typically has a young age at presentation (20–40 years: mean age ~27 years) when compared to conventional HCC. Unlike the more common HCC, patients most often do not have coexistent liver disease such as cirrhosis.

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.

Fibrolamellar hepatocellular carcinoma (FHCC) is a rare form of hepatocellular carcinoma (HCC) that typically affects young adults and is characterized, under the microscope, by laminated fibrous layers interspersed between the tumour cells. Approximately 200 new cases are diagnosed worldwide each year.

Liver tumors or hepatic tumors are tumors or growths on or in the liver (medical terms pertaining to the liver often start in "hepato-" or "hepatic" from the Greek word for liver, "hepar"). Several distinct types of tumors can develop in the liver because the liver is made up of various cell types. These growths can be benign or malignant (cancerous). They may be discovered on medical imaging (even for a different reason than the cancer itself), or may be present in patients as an abdominal mass, hepatomegaly, abdominal pain, jaundice, or some other liver dysfunction.

Pancreatic cancer is the fifth-most-common cause of cancer deaths in the United States, and the seventh most common in Europe. In 2008, globally there were 280,000 new cases of pancreatic cancer reported and 265,000 deaths. These cancers are classified as endocrine or nonendocrine tumors. The most common is ductal adenocarcinoma. The most significant risk factors for pancreatic cancer are advanced age (over 60) and smoking. Chronic pancreatitis, diabetes or other conditions may also be involved in their development. Early pancreatic cancer does not tend to result in any symptom, but when a tumor is advanced, a patient may experience severe pain in the upper abdomen, possibly radiating to the back. Another symptom might be jaundice, a yellowing of the skin and eyes.

Pancreatic cancer has a poor prognosis, with a five-year survival rate of less than 5%. By the time the cancer is diagnosed, it is usually at an advanced, inoperable stage. Only one in about fifteen to twenty patients is curative surgery attempted. Pancreatic cancer tends to be aggressive, and it resists radiotherapy and chemotherapy.

Adult survivors of childhood cancer have some physical, psychological, and social difficulties.

Premature heart disease is a major long-term complication in adult survivors of childhood cancer. Adult survivors are eight times more likely to die of heart disease than other people, and more than half of children treated for cancer develop some type of cardiac abnormality, although this may be asymptomatic or too mild to qualify for a clinical diagnosis of heart disease.

Familial and genetic factors are identified in 5-15% of childhood cancer cases. In <5-10% of cases, there are known environmental exposures and exogenous factors, such as prenatal exposure to tobacco, X-rays, or certain medications. For the remaining 75-90% of cases, however, the individual causes remain unknown. In most cases, as in carcinogenesis in general, the cancers are assumed to involve multiple risk factors and variables.

Aspects that make the risk factors of childhood cancer different from those seen in adult cancers include:

- Different, and sometimes unique, exposures to environmental hazards. Children must often rely on adults to protect them from toxic environmental agents.

- Immature physiological systems to clear or metabolize environmental substances

- The growth and development of children in phases known as "developmental windows" result in certain "critical windows of vulnerability".

Also, a longer life expectancy in children avails for a longer time to manifest cancer processes with long latency periods, increasing the risk of developing some cancer types later in life.

There are preventable causes of childhood malignancy, such as delivery overuse and misuse of ionizing radiation through computed tomography scans when the test is not indicated or when adult protocols are used.

There are several types of benign liver tumor.

Hemangiomas: These are the most common type of benign liver tumor, found in up to 7% of autopsy specimens. They start in blood vessels. Most of these tumors do not cause symptoms and do not need treatment. Some may bleed and need to be removed if it is mild to severe. A rare tumor is Infantile hemangioendothelioma.

Hepatic adenomas: These benign epithelial liver tumors develop in the liver and are also an uncommon occurrence, found mainly in women using estrogens as contraceptives, or in cases of steroid abuse. They are, in most cases, located in the right hepatic lobe and are frequently seen as solitary. The size of adenomas range from 1 to 30 cm. Symptoms associated with hepatic adenomas are all associate with large lesions which can cause intense abdominal pain. Over the last few decades there has been an increase with occurrences of this specific type of adenoma. The prognosis for these tumors has still not been mastered. Some correlations have been made such as malignant transformation, spontaneous hemorrhage, and rupture.

Focal nodular hyperplasia (FNH) is the second most common tumor of the liver. This tumor is the result of a congenital arteriovenous malformation hepatocyte response. This process is one in which all normal constituents of the liver are present, but the pattern by which they are presented is abnormal. Even though those conditions exist the liver still seems to perform in the normal range. Other types include nodular regenerative hyperplasia and hamartoma.

"Breastfeeding jaundice" or "lack of breastfeeding jaundice," is caused by insufficient breast milk intake, resulting in inadequate quantities of bowel movements to remove bilirubin from the body. This leads to increased enterohepatic circulation, resulting in increased reabsorption of bilirubin from the intestines. Usually occurring in the first week of life, most cases can be ameliorated by frequent breastfeeding sessions of sufficient duration to stimulate adequate milk production.

OPA has been found in most countries where sheep are farmed, with the exception of Australia and New Zealand. OPA has been eradicated in Iceland.

No breed or sex of sheep appears to be predisposed to OPA. Most affected sheep show signs at 2 to 4 years of age.

OPA is not a notifiable disease, and therefore it is difficult to assess its prevalence.

Whereas breastfeeding jaundice is a mechanical problem, breast milk jaundice is a biochemical occurrence and the higher bilirubin possibly acts as an antioxidant. Breast milk jaundice occurs later in the newborn period, with the bilirubin level usually peaking in the sixth to 14th days of life. This late-onset jaundice may develop in up to one third of healthy breastfed infants.

- First, at birth, the gut is sterile, and normal gut flora takes time to establish. The bacteria in the adult gut convert conjugated bilirubin to stercobilinogen which is then oxidized to stercobilin and excreted in the stool. In the absence of sufficient bacteria, the bilirubin is de-conjugated by brush border β-glucuronidase and reabsorbed. This process of re-absorption is called enterohepatic circulation. It has been suggested that bilirubin uptake in the gut (enterohepatic circulation) is increased in breast fed babies, possibly as the result of increased levels of epidermal growth factor (EGF) in breast milk. Breast milk also contains glucoronidase which will increase deconjugation and enterohepatic recirculation of bilirubin.

- Second, the breast-milk of some women contains a metabolite of progesterone called 3-alpha-20-beta pregnanediol. This substance inhibits the action of the enzyme uridine diphosphoglucuronic acid (UDPGA) glucuronyl transferase responsible for conjugation and subsequent excretion of bilirubin. In the newborn liver, activity of glucuronyl transferase is only at 0.1-1% of adult levels, so conjugation of bilirubin is already reduced. Further inhibition of bilirubin conjugation leads to increased levels of bilirubin in the blood. However, these results have not been supported by subsequent studies.

- Third, an enzyme in breast milk called lipoprotein lipase produces increased concentration of nonesterified free fatty acids that inhibit hepatic glucuronyl transferase, which again leads to decreased conjugation and subsequent excretion of bilirubin.

OPA has been used as an animal model for human lung cancer, because OPA is histologically similar to human adenocarcinoma in situ of the lung.

As of 2013 there had been case reports of using HPV vaccines to prevent laryngeal papillomatosis but it was not known if this was effective. As of 2015 use of the measles-mumps-rubella vaccine to reduce rate of recurrences had been investigated, but had not yielded significant results.

Use of telomerase inhibitors such as Imetelstat seem to have very low toxicity compared to other chemotherapy. The only known side effect of most telomerase inhibitors is dose-induced neutropenia. Neuropsychological deficits can result from resection, chemotherapy, and radiation, as well as endocrinopathies. Additionally, an increase in gastrointestinal complications has been observed in survivors of pediatric cancers.

The evolution of laryngeal papillomatosis is highly unpredictable and is characterized by modulation of its severity and variable rate of progression across individuals. While instances of total recovery are observed, the condition is often persistent and lesions can reappear even after treatment. Factors that might affect the clinical course of the condition include: the HPV genotype, the age at onset, the elapsed time between the diagnosis and first treatment in addition to previous medical procedures. Other factors, albeit controversial, such as smoking or the presence gastroesophageal reflux disease might also play a role in the progression of the disease.

The papillomas can travel past the larynx and infect extralaryngeal sites. In more aggressive cases, infection of the lungs can occur with progressive airway obstruction. Although rare (less than 1% of people with laryngeal papillomatosis), transformation from a benign form to a malignant form is also observed. Death can result from these complications (morbidity rate is around 1-2%).

The 5-year disease-free survival for age >5 years is 50-60%. Another report found a similar 5-year survival at about 65% with 51% progression-free survival. The 10-year disease-free survival is 40-50%. Younger ages showed lower 5 and 10-year survival rates. A 2006 study that observed 133 patients found 31 (23.3%) had a recurrence of the disease within a five-year period.

Gilbert's syndrome and G6PD deficiency occurring together especially increases the risk for kernicterus.

Renal cysts and diabetes syndrome (RCAD), also known as MODY 5, is a form of maturity onset diabetes of the young.

HNF1β-related MODY is one of the less common forms of MODY, with some distinctive clinical features, including atrophy of the pancreas and several forms of renal disease. HNF1β, also known as transcription factor 2 (TCF2), is involved in early stages of embryonic development of several organs, including the pancreas, where it contributes to differentiation of pancreatic endocrine Ngn3 cell progenitors from non-endocrine embryonic duct cells. The gene is on chromosome 17q.

The degree of insulin deficiency is variable. Diabetes can develop from infancy through middle adult life, and some family members who carry the gene remain free of diabetes into later adult life. Most of those who develop diabetes show atrophy of the entire pancreas, with mild or subclincal deficiency of exocrine as well as endocrine function.

The non-pancreatic manifestations are even more variable. Kidney and genitourinary malformation and diseases may occur, but inconsistently even within a family, and the specific conditions include a range of apparently unrelated anomalies and processes. The most common genitourinary condition is cystic kidney disease, but there are many varieties even of this. Renal effects begin with structural alterations (small kidneys, renal cysts, anomalies of the renal pelvis and calices), but a significant number develop slowly progressive renal failure associated with chronic cystic disease of the kidneys. In some cases, renal cysts may be detected in utero. Kidney disease may develop before or after hyperglycemia, and a significant number of people with MODY5 are discovered in renal clinics.

With or without kidney disease, some people with forms of HNF1β have had various minor or major anomalies of the reproductive system. Male defects have included epididymal cysts, agenesis of the vas deferens, or infertility due to abnormal spermatozoa. Affected women have been found to have vaginal agenesis, hypoplastic, or bicornuate uterus.

Liver enzyme elevations are common, but clinically significant liver disease is not. Hyperuricaemia and early onset gout have occurred.

Kernicterus is a bilirubin-induced brain dysfunction. The term was coined in 1904 by Schmorl. Bilirubin is a naturally occurring substance in the body of humans and many other animals, but it is neurotoxic when its concentration in the blood is too high, a condition known as hyperbilirubinemia. Hyperbilirubinemia may cause bilirubin to accumulate in the grey matter of the central nervous system, potentially causing irreversible neurological damage. Depending on the level of exposure, the effects range from clinically unnoticeable to severe brain damage and even death.

When hyperbilirubinemia increases past a mild level, it leads to jaundice, raising the risk of progressing to kernicterus. When this happens in adults, it is usually because of liver problems. Newborns are especially vulnerable to hyperbilirubinemia-induced neurological damage, because in the earliest days of life, the young and still-developing liver is heavily exercised by the breakdown of fetal hemoglobin as it is replaced with adult hemoglobin. Mildly elevated serum bilirubin levels are common in newborns, and neonatal jaundice is not unusual, but bilirubin levels must be carefully monitored in case they start to climb, in which case more aggressive therapy is needed, usually via light therapy but sometimes even via exchange transfusion.