The Cuban diplomats were asked to leave their embassy on May 23, State Department spokeswoman Heather Nauert said at a briefing, without specifying the number of Americans affected by these symptoms or detailing their nature.
A report by US broadcaster CNN suggests the symptoms were related to an "acoustic attack" from sonic devices, citing senior State Department officials at the US embassy.
"We first heard of these incidents back in late 2016," Nauert said.
"Some US government personnel who were working at our embassy in Havana, Cuba ... reported some incidents which have caused a variety of physical symptoms. We don't have any definitive answers about the source or the cause of what we consider to be incidents," she said.
She added: "We had to bring some Americans home or some Americans chose to come home as a result of that. And as a result of that, we've asked two Cubans to leave the United States and they have."
Later Wednesday, the Cuban government confirmed the report.
It said it had objected to the expulsion of its officials, while also urging the United States to work together to shed light on the incidents earlier this year in Havana.
Relations between the US and Cuba were restored in 2015 after a half-century break by then US president Barack Obama and his Cuban counterpart Raul Castro.
But the rapprochement was partially rolled back by Obama's successor Donald Trump who in June announced tightened rules for Americans traveling to Cuba, banned ties with a military-run tourism firm and reaffirmed the existing US trade embargo.
