Pregnant women have been warned not to travel to the Games in Rio de Janeiro because the mosquito-borne virus can cause birth defects and lead to developmental problems in babies.
But van Garderen, who would have been considered among the favourites for both the road race and the hilly time trial, is not willing to risk bringing the disease back from Brazil.
"Although the risks associated with the Zika virus can be minimal and precautions can be taken, my wife Jessica is pregnant, and I don't want to risk bringing anything back that could potentially have an effect," Van Garderen said in a statement through USA Cycling.
"If circumstances were different I would have loved to be selected again to represent the USA, but my family takes priority and it's a decision that I'm completely comfortable with.
"I hope that I'll be in the position to race at the 2020 Olympic Games."
Tejay van Garderen's BMC Timemachine
Van Garderen is the first American athlete, and the first cyclist, to confirm he will not be attending the Olympics because of Zika. Golfer Rory McIlroy said that he was monitoring the threat of the disease but has subsequently said his fears had eased.
The World Health Organization revised its guidance for people travelling to countries where Zika is prevalent, stating that people should wait a full eight weeks to have unprotected sex or attempt to conceive a baby, after returning, even if they show no symptoms of the disease.
Men who show symptoms of Zika should practice safe sex or abstain completely for at least six months, the new guidelines state.
Last week, 150 public health experts wrote an open letter to WHO calling for the Games to be moved or cancelled, but this was rejected by the organisation.
Stuart Clarke is a News Associates trained journalist who has worked for the likes of the British Olympic Associate, British Rowing and the England and Wales Cricket Board, and of course Cycling Weekly. His work at Cycling Weekly has focused upon professional racing, following the World Tour races and its characters.
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