A study reported in Human Reproduction in 2001 showed that of the babies born to IVF in the period 1992-1997 in Sweden (some 9111 children), that there was no increase risk of congenital malformations amongst IVF children, that there was a 3-fold increase risk of neural tube defects, alimentary atresia, omphalocele and hypospadias (after ICSI only).
The authors concluded that the "absolute risk for a congenital malformation association with IVF is small".
Source: Human Reproduction Vol.16, No.3 pp. 504-509, 2001
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