Factor V deficiency affects an estimated 1 in 1 million people. This condition is more common in countries such as Iran and southern India, where it occurs up to ten times more frequently than in western countries.

Factor V deficiency is usually caused by mutations in the F5 gene, which provides instructions for making a protein called coagulation factor V. This protein plays a critical role in the coagulation system, which is a series of chemical reactions that forms blood clots in response to injury. F5 gene mutations that cause factor V deficiency prevent the production of functional coagulation factor V or severely reduce the amount of the protein in the bloodstream. People with this condition typically have less than 10 percent of normal levels of coagulation factor V in their blood; the most severely affected individuals have less than 1 percent. A reduced amount of functional coagulation factor V prevents blood from clotting normally, causing episodes of abnormal bleeding that can be severe.

Very rarely, a form of factor V deficiency is caused by abnormal antibodies that recognize coagulation factor V. Antibodies normally attach (bind) to specific foreign particles and germs, marking them for destruction, but the antibodies in this form of factor V deficiency attack a normal human protein, leading to its inactivation. These cases are called acquired factor V deficiency and usually occur in individuals who have been treated with substances that stimulate the production of anti-factor V antibodies, such as bovine thrombin used during surgical procedures. There is no known genetic cause for this form of the condition.