It is common knowledge that inbreeding results in genetic problems; inbred offspring are likely to suffer from multiple genetic defects and are often subject to mental retardation or disease.

All organisms have some of the genetic flaws that cause these syndromes. These alleles rarely manifest themselves in the phenotype, however, because they are recessive; there is usually a dominant allele to counter the negative effects. But when these genes mix with close relatives, the frequencies of the rare, harmful recessive alleles increase; they eventually become common within the inbred population. Even if a particular bad allele fails to dominate, the gene pool is easily big enough to supply replacements. The genetic defects are compounded in this way until the offspring have serious problems; often the inbred offspring do not survive. A famous example is the hemophilia that arose among the royal family of England. After generations of inbreeding, hemophilia suddenly became very common within the family; many of Queen Victoria's children suffered from this disorder, most notably Prince Leopold, who died young from a short fall.

Inbreeding occurs when mating individuals share a common ancestor that is more recent than would be expected in a randomly-mating population.

Thus, a mating between cousins would entail a common ancestor by two generations -- a mutual grandparent. In a population in which inbred mating is uncommon, any random pair of individuals most probably has a much older common ancestor. Because the common ancestor of an inbred pair is more recent, there is a greater chance that the pair also have alleles in common (see identity by descent). This has the consequence of making many loci homozygous. Note: inbreeding does not directly change the frequency of alleles in the population; it only changes the frequency of genotypes.

Although the exposure of deleterious alleles in homozygotes often creates a loss of fitness in the population, inbreeding is not inherently harmful. It is simply expressing genetic variation that was previously concealed in heterozygote carriers. In populations where inbreeding has been frequent for many generations, deleterious alleles exist at lower frequencies, having been purged from the population by natural selection acting on homozygotes. Nevertheless, inbreeding depression may be responsible for the ubiquity of incest taboo in human populations. Indeed, children produced from matings between human relatives are roughly ten times more likely to express congenital disease.

Hidden inbreeding, also called unconscious inbreeding, occurs when a child is produced by a man and a woman unaware that they are already related to each other. While technically we are all related, this refers to a relationship close enough to have potential detrimental effects for the offspring.

One example of this is the inbreeding that occurred from the seventeenth through twentieth centuries on Martha's Vineyard, which resulted in a large deaf population on the island. The Vineyard community was very isolated for most of that time, and as a result the only taboo marriages were between aunts and nephews, uncles and nieces, and siblings - first cousins and beyond were fair game. By the 1970s, members of one clan insisted they were unrelated despite sharing a last name, yet those people could be traced back to the same individual from the original group of settlers on the island.

Source: Groce, Nora Ellen. Everyone Here Spoke Sign Language. Page 44.