Hemophilia (Types A and B) are have chromosomal x-linked recessive inheritance. This means that it is carried on the x chromosome and it will yield to a normal, dominant trait. Since women posess two x chromosomes, usually if the trait is carried in a woman, a woman will have a dominant normal chromosome and a recessive abnormal chromosome. Therefore, it can be passed on, but it does not, under normal circumstances, affect her. Males however, only have one x chromosome (and a y). Therefore, they can be affected by one recessive trait, because there is no dominant to mask it. Males cannot pass it to their sons, as their sons receive a y from their father, the x coming from their mother. Males can pass the gene to their daughters, resulting in their daughters becoming carriers (however if the mother passes the gene to the daughter as well, she will be a hemophiliac). The gene is therefore carried my women, but affects males.

The genes are carried on the chromosome. Genes are what tells the ribosomes of a cell to create proteins. Since this gene is defective, is incorrectly "tells" the ribosome how to make the protein of either factor VIII or factor IX (VIII being type A or IX being type B), or perhaps doesn't even tell it how to make it at all. That is the relationship. The protein is essential in forming blood clots, thus the symptoms of hemophilia.

Hemophilia C, however, is autosomal. This means it is not sex-linked, however, the relationship of genes and proteins are on the same level.