The study, which compared the outcomes of hundreds of thousands of births, looked at the risk of stillbirth, low birth weight, premature birth and infant death.
Both traditional IVF, involving fertilisation in a glass dish, and the injection of sperm directly into eggs increased the chances of complications, the researchers found.
Scientists from Adelaide University, Australia, studied 17 years of data from more than 300,000 births in South Australia, of which 4300 were the result of assisted reproduction.
Study leader Professor Michael Davies said: "Compared with spontaneous conceptions in couples with no record of infertility, singleton babies from assisted conception were almost twice as likely to be stillborn, more than twice as likely to be pre-term, almost three times as likely to have very low birth weight, and twice as likely to die within the first 28 days of birth."
The study also looked at birth outcomes for women who found it hard to get pregnant but never received intensive fertility treatment. Their chances of experiencing complications were much higher than average.
But a British fertility expert stressed many of the problems may be related to patients' infertility rather than IVF treatment.
Sheena Lewis, of Queen's University, Belfast, said: "We have known for some time that couples conceiving spontaneously after a period of infertility have poorer outcomes. This indicates these problems may come from the disease rather than the fertility treatment.