It was not immediately clear what had happened, with spokeswoman Heather Nauert saying there were no "definitive answers about the source or cause".
But Ms Nauert refused to be drawn further on what the symptoms were.
But one source told the Associated Press news agency the symptoms reported included hearing loss.
It was suggested the hearing loss could have been caused by some kind of sonic device placed outside the diplomats' homes, emitting inaudible sound waves that can cause deafness.
Staff began complaining of the strange symptoms late last year, Ms Nauert said.
While they were not life-threatening, she revealed a number of people had been brought home to the US as a result.
Ms Nauert said the government was taking it "very seriously, and there is an investigation currently under way".
It is understood that the two expelled Cuban diplomats left Washington DC in May, the BBC's Will Grant reports from Havana.
So far, their government has not responded to the reports.
Washington and Havana only re-established ties in 2015, following 50 years of hostilities between the two countries.

The student and a male friend she was travelling with were beaten, stripped and thrown off the bus in the attack on Sunday evening.
The couple have been admitted to hospital, where the woman is said to be in a critical condition.
Police have arrested the driver of the bus and detained several people.
Delhi's rape figures are higher than for other Indian cities of comparable size, correspondents say.
City shamed, headlined The Times of India, saying that Sunday's incident is a "new low for a city already notorious as India's rape capital".
Savagery Shames City, headlined Mail Today, adding that "horror had revisited the streets of the capital" on Sunday night.
The newspaper said that 582 cases of rape had been reported in Delhi so far this year.
Delhi Shamed Again, said The Pioneer, saying the incident had "again renewed focus on the dismal state of safety for girls and women who venture out at night".
The Indian Express said the bus was driven around on a stretch in south Delhi for more than an hour and had "crossed" three police patrol vans.
The Chief Minister of Delhi Sheila Dikshit told The Hindu newspaper that this was a "shockingly extraordinary case".
"We want to ensure that the culprits are not granted bail under any circumstances. Stringent punishment for them is the need of the hour," she said.
Mrs Dikshit said she would be considering the setting up of a fast track court to "ensure speedy justice to the victim".
The woman and her friend had boarded the bus from Munirka area and were on their way to Dwarka in south-west Delhi.
They were returning after watching a film in a shopping centre in south Delhi, police said.
The couple were attacked by "at least four men", police said.
Washington has expelled two Cuban diplomats after US embassy staff in Havana suffered mysterious physical symptoms, the US state department said.
[NEXT_CONCEPT]
There has been shock and outrage in India over the gang rape of a 23-year-old student on a city bus in the capital, Delhi.