The U.S. CDC said in a statement it reached the conclusion after "careful review of existing evidence" using established scientific criteria.
"This study marks a turning point in the Zika outbreak. It is now clear that the virus causes microcephaly," said Tom Frieden, director of the U.S. agency.
Frieden said the U.S. CDC is launching further studies to determine whether microcephaly, or abnormally small heads, is only "the tip of the iceberg of what we could see in damaging effects on the brain and other developmental problems."
The conclusion, published in the New England Journal of Medicine, means that a woman infected with Zika during pregnancy has an increased risk of having a baby with these health problems, the CDC said.
It does not mean, however, that all women who have Zika virus infection during pregnancy will have babies with problems, it continued.
"As has been seen during the current Zika outbreak, some infected women have delivered babies that appear to be healthy," the CDC statement said.
The CDC report noted many questions remain including the spectrum of defects caused by prenatal Zika infection, the degree of relative and absolute risks of adverse outcomes among fetuses whose mothers were infected at different times during pregnancy, and factors that might affect a woman's risk of adverse pregnancy or birth outcomes.
"Addressing these questions will improve our ability to reduce the burden of the effects of Zika virus infection during pregnancy," the report wrote.
Zika is transmitted primarily through the bite of an infected Aedes species mosquito, which also spreads chikungunya, and dengue.
Symptoms include fever, rash, joint pain and red eyes, but severe disease requiring hospitalization is uncommon and case fatality is low.
There is now no vaccine or medicine available for Zika virus. (Xinhua)