Carrying out checks on embryos for genetic disorders incurs no more risk than standard IVF, researchers suggest.
In PGD, a cell is taken from an embryo at the eight-cell stage
The latest study from Brussels' Free University looked at the outcomes of 583 children born after preimplantation genetic diagnosis (PGD).
There have been safety questions over this procedure because it is relatively new and involves removing a cell from an embryo at around three days old.
The work was presented at a European Society of Human Genetics meeting.
PGD was first introduced in 1990 as an experimental procedure.
It checks fertilised eggs for genetic disorders so that an unaffected embryo can be implanted into the mother's womb, as with conventional IVF.
The UK's fertility watchdog the HFEA has licensed PGD for more than 50 genetic conditions.
Researchers around the world have been tracking the progress of PGD babies to monitor the long-term sequelae.
In the Belgian study group, 563 of the 583 PGD babies were born alive.
These babies had a comparable birth weight to those born after conventional IVF treatment alone, and another fertility procedure called ICSI - where sperm is injected directly into an egg.
At two months, and again at two years of age, these children appeared to be equally healthy - the rate of birth defects or malformations was comparable between the groups.
Lead researcher Professor Ingeborg Liebaers, from the Research Centre for Reproductive Genetics at the Université Libre de Bruxelles, said: "We were encouraged to find that the major malformation rate was no higher than that which is found in children born after conventional IVF and ICSI."
But she said they needed to further investigate the perinatal death rate, which was higher than in IVF and ICSI babies.
Most of these deaths were multiple pregnancies, such as twins or triplets, which might be important, say the authors.
Professor Alan Handyside, a spokesman for the British Fertility Society - and the pioneer of PGD with Professor Lord Robert Winston at Hammersmith Hospital, London in the late eighties - said the results were reassuring.
"We were confident when we first started doing PGD that we wouldn't cause any abnormalities.
"So I'm very reassured and not at all surprised by these latest results."
However, he said it would take several more decades to look at the longer-term outcomes. The oldest PGD children are approaching 17 years.
He said the perinatal death rate was unexpected and should be investigated. He said it could be a statistical anomaly.
Professor Handyside said that any medical procedure carried a risk and that this had to be weighed against the benefits - PGD can reveal which embryos could develop fatal or debilitating diseases.
Critics oppose the idea of being able to screen out disorders.
And concerns have been raised about the possible genetic risk to children born using assisted reproduction techniques such as IVF because of the manipulation of the egg and sperm during the process.
The BFS says there is no conclusive data to link IVF with any specific abnormality, although some recent studies have shown an increase in "imprinting" disorders which can lead to intellectual impairment.
It says: "These are normally very rare disorders and the recent data indicates that although they may be increased as a result of IVF they are still rare.
"At this time we cannot conclusively say whether or not there is a cause and effect relationship between IVF/ICSI and specific abnormalities, however, it is clear that, if such a risk exists, it is small and that further monitoring of children resulting from such treatment is necessary to answer this question."
PGD is a relatively rare procedure, used in fewer than 200 of the 40,000 cycles of IVF carried out in the UK each year.