The most common complication of hemophilia is arthritis or permanent joint damage due to repeated bleeding within the joint. This can cause long-term pain and loss of mobility.

Some people with hemophilia can develop antibodies to the replacement clotting factors used to treat the condition. The antibodies can destroy the clotting factor before it has a chance to work. This can be a serious problem as it means that the main treatment for hemophilia is no longer effective. When antibodies develop, doctors may use larger doses of clotting factor or try different types of factor. Antibodies to clotting factor develop in about 20% of those with severe hemophilia A, and about 1% of those with hemophilia B.

Before the dangers of the AIDS epidemic were fully recognized, blood containing the HIV virus was used to produce replacement clotting factors and many hemophiliacs acquired the disease between 1979 and 1985. Hepatitis has also been a problem in the past, with many hemophiliacs contracting the disease from blood carrying the virus.

Blood donors are now carefully screened and all donated blood products tested for these viruses. Blood products used to create clotting factors are treated with a detergent and heated to destroy viruses. Vaccination against hepatitis A and B is also offered to all hemophiliacs. In recent years synthetic alternatives to clotting factors made from human blood have become available. Known as recombinant clotting factors, they are regarded as free from the risk of any blood infections as well as the theoretical risk from Creutzfeldt-Jakob disease (CJD).