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.
Washington has expelled two Cuban diplomats after US embassy staff in Havana suffered mysterious physical symptoms, the US state department said.