From: http://www.pffd.org/what_causes_pffd.htm
The process of formation and development of the fetus is called morphogenesis. It is a very delicate phase, because the position of each cell is crucial for the proper development of tissues and everything around him. If morphogenesis is disturbed by some external factor, the time at which this occurs is decisive for the type of defect that could have. If something happens at an early stage, then one speaks of "malformation", unlike the "deformation", which usually takes place at a later stage and arises from mechanical factors.

In the fetus the limb buds develop within the first 28 to 32 days of pregnancy and in 33-36 days, the flat foot is visible. If something affects the growth of the fetus during this critical stage of formation of the limbs (which lasts from 4 to 6 weeks), this can cause PFFD.
That thing that causes malformation of an embryo or a fetus is called a "teratogen." The teratogenic for PFFD is unknown. PFFD is not a genetic disease.
Some suppose that could be caused by anoxia (lack of oxygen), ischemia (temporary shortage of blood supply), from chemical products, hypothermia, radiation, bacterial toxins, viral infections, and enzyme changes ormonali.
In realtá l'unica causa accertata é il farmaco Talidomide, che è stato commercializzato come un sedativo, sonnifero, e per i disturbi da gravidanza (purtroppo), prima di essere tolto dal mercato nei primi anni 1960.
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