Intrahepatic cholestasis of pregnancy is estimated to affect 1 percent of women of Northern European ancestry. The condition is more common in certain populations, such as women of Araucanian Indian ancestry in Chile or women of Scandinavian ancestry. This condition is found less frequently in other populations.

Genetic changes in the ABCB11 or the ABCB4 gene can increase a woman's likelihood of developing intrahepatic cholestasis of pregnancy.

The ABCB11 gene provides instructions for making a protein called the bile salt export pump (BSEP). This protein is found in the liver, and its main role is to move bile salts (a component of bile) out of liver cells, which is important for the normal release of bile. Changes in the ABCB11 gene associated with intrahepatic cholestasis of pregnancy reduce the amount or function of the BSEP protein, although enough function remains for sufficient bile secretion under most circumstances. Studies show that the hormones estrogen and progesterone (and products formed during their breakdown), which are elevated during pregnancy, further reduce the function of BSEP, resulting in impaired bile secretion and the features of intrahepatic cholestasis of pregnancy.

The ABCB4 gene provides instructions for making a protein that helps move certain fats called phospholipids across cell membranes and release them into bile. Phospholipids attach (bind) to bile acids (another component of bile). Large amounts of bile acids can be toxic when they are not bound to phospholipids. A mutation in one copy of the ABCB4 gene mildly reduces the production of ABCB4 protein. Under most circumstances, though, enough protein is available to move an adequate amount of phospholipids out of liver cells to bind to bile acids. Although the mechanism is unclear, the function of the remaining ABCB4 protein appears to be impaired during pregnancy, which may further reduce the movement of phospholipids into bile. The lack of phospholipids available to bind to bile acids leads to a buildup of toxic bile acids that can impair liver function, including the regulation of bile flow.

Most women with intrahepatic cholestasis of pregnancy do not have a genetic change in the ABCB11 or ABCB4 gene. Other genetic and environmental factors likely play a role in increasing susceptibility to this condition.