A heart murmur is heard when blood passes through an opening that makes it turbulent. Could be caused by defective valves (stenotic or prolapse/insufficient), holes that should be closed (atrial/ventricle septums), or unusual connections (patent ductus arteriosis).
It is not uncommon for newborns to have a patent ductus arteriosis (embryonic connection between aortic arch and pulmonary artery)--this could cause a murmur but is usually beningn and will close on its own or with indomethacin. Newborn could have patent foramen ovale (between left and right atria)--this is also usually benign.
Other causes of heart murmurs in newborns:
1. Ventricular septal defect
2. congenital bicuspid aortic valve
3. tetralogy of fallot (pulmonic stenosis, overiding aorta, ventricular septal defect, right ventricular hypertrophy)
many many others......I can't remember without digging up books/notes.
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