There are many. There are many differences. Omphalocele is a defect at the umbilical ring, usually has an amniotic sac covering the organs, and can be associated with many other congenital anomalies. Gastroschisis is usually a defect on the right of the umbilical cord, does not have a sac, and usually not associated with many congenital anomalies.
Location. These are both birth defects where the intestine comes out of the abdominal wall through a defect. An omphalocele will be covered by a membrane, and there is a higher risk of other birth defects with this condition. Here are some links: http://www.Ncbi.Nlm.Nih.Gov/pubmedhealth/pmh0001987/ http://www.Ncbi.Nlm.Nih.Gov/pubmedhealth/pmh0001989/.