Compared with 'natural' conception, IVF overall had no effect on autism rates and led to a very small 18% increased risk of low IQ which appeared to be linked to multiple births.
The significant findings only emerged when researchers compared six different types of IVF involving the standard "mixing-in-a-dish" method of fertilising eggs or Intra-Cytoplasmic Sperm Injection (Icsi).
Icsi used with fresh or frozen embryos produced 51% more intellectually impaired children than standard IVF.
The direct injection method, Icsi, was originally developed to help infertile men, but it now makes up half of IVF treatments in the UK including those resulting from female fertility problems.
Certain forms of IVF treatment are significantly associated with an increased risk of low intelligence in children, a major study has shown.
A link was also found with an especially severe type of autism, but only in the case of twins or triplets.
Scientists who analysed data on more than 2.5 million births stressed that the chances of an IVF baby being affected remained tiny in real terms.
The Swedish study, published in the Journal of the American Medical Association, is the first of its kind to compare a wide range of IVF treatments.
Britain may become the first country in the world to allow babies to be born with three genetic parents to help stamp out serious diseases.Read the full story ›
Paul Tully from the Society for the Protection of Unborn Children said the "three parent" IVF technique is a "step" towards designer babies.
Mr Tully told ITV News: "It is a change that can be passed on to future generations, and we are manipulating the genes of a child.
"We're concerned that we are replacing what we know to be defective DNA in the embryos that we don't like with what we think is good DNA - but we can't be sure.
"Putting the money into this kind of research is denying funding to research which is needed and ongoing to help people with mitochondrial diseases and other diseases in other ways.
"We've seen the same thing before with stem cell research, we've seen it with IVF - promises that using embryos will lead to advances but come to nothing.
Dr David King, director of Human Genetics Alert, told ITV News the "three parent" IVF technique crosses a "crucial ethical line":
Genetic Alliance UK has welcomed the "three parent" IVF technique proposal.
The charity's director, Alastair Kent, said: "Many of these [mitochondrial] conditions are so severe that they are lethal in infancy, creating a lasting impact upon the child's family.
"An added option for families at risk of having a child with such a condition is welcome".
Experts said the technique would likely be used in around a dozen IVF cases every year.
The director of the Human Genetics Alert campaign group said the IVF technique used to create babies with three genetic parents is "unnecessary" and "ethically unsound".
Dr David King also criticised the Government for failing to conduct a more comprehensive public consultation on the issue.
Dr King told Reuters, "They cross the ethical line that has been agreed by Governments around the world that we should not genetically alter human beings".
Some groups say the proposals for three parent babies are causing worldwide concern:
These techniques are unnecessary and unsafe and were in fact rejected by the majority of consultation responses.
It is a disaster that the decision to cross the line that will eventually lead to a eugenic designer baby market should be taken on the basis of an utterly biased and inadequate consultation.
Such a decision of major historical significance requires a much more extensive public debate with a much clearer outcome.
We therefore call upon the Secretary of State for Health not to legalise the techniques until a major national debate has taken place and the outcome is much clearer.
The Chief Medical Officer for England, Professor Dame Sally Davies, explains that the 'three parent' technique does not tamper with the nucleus. It simply moves it into a cell which has healthy 'battery packs', known as mitochondria, which power the nucleus properly and eradicate serious disease.
A recent public consultation found that 56% of those questioned were "very" or "fairly" positive about the treatments. Patient focus groups were said to be "extremely positive". Experts are also behind the procedures.
Scientists have developed ground-breaking new procedures which could stop these diseases being passed on, bringing hope to many families seeking to prevent their future children inheriting them.
It's only right that we look to introduce this life-saving treatment as soon as we can. What we're going to do now is start to develop the regulations, to consult on the regulations, and then to take them into Parliament.