Othman al-Bizanti, the lawyer for the defence, said that his clients were innocent and were awaiting the verdict "with anguish".
Earlier in the year a British scientific journal published a report saying the particular strain of the HIV virus which infected the children was introduced to the hospital before the six began working there.
Many believe the infections were caused by bad hygiene at the hospital.
Since the original accusations, 52 of the infected children have died.
Prior to the accusations there had been no confirmed cases of the virus in Libya.
Thrown out of court
In 1999, six Bulgarian nurses and two doctors, one Bulgarian and one Palestinian, were detained on charges of deliberately infecting children with the HIV virus.
|The EU has called for the release |
of the six health workers
The health workers pleaded not guilty and in 2002 the case was thrown out of court, but a second prosecution is started and three of the defendants withdraw confessions, saying they had been tortured and forced to write them.
In 2004 the five nurses and Palestinian doctor were sentenced to death by firing squad, but the ruling was quashed by the Libyan supreme court.
The Bulgarian doctor was charged with currency smuggling and sentenced to four years in prison.
In 2006, an appeal court ordered a retrial of the six remaining health workers.
Relations with the US
On Friday, David Welch, the US assistant secretary of state, visited Libya to discuss the country's relations with the US as well as the case of the health workers.
A senior US official stressed that Tuesday's verdict will not be the final step in the Libyan legal process.
He said it could be appealed against to the supreme court and could then go to the Libyan higher judicial council, which might grant clemency.