By and large, the incidence of microtia in the general population is sporadic, with no definitive cause. The only attributable causes are cases in which the mother contracted rubella or influenza during the first trimester or used thalidomide, isotretinoin (Accutane), clomid, retinoic acid or misoprostol during the first trimester. In addition hypoxia is a potential cause, either from living at high elevations or from placental steal, in which a twin has a larger placenta and effectively steals oxygen and nutrients from the affected twin.
A multifactorial collection of hereditary traits seems to be in part responsible for the occurrence of microtia, as opposed to a chromosomal aberration. In an intensive study by Takahashi, patients with microtia had a 5.7% chance of someone in their immediate family of parents, siblings, aunts, uncles and grandparents presenting with auricular deformities. If distant relatives were included, that percentage reached 10.5%. In effect, if a family has already had one child with microtia, there is a 1 in 20 chance that their second child will also be affected.
The ultimate takeaway is that the incidence of microtia is a sporadic event, over which the parents had very little control.