An international team analysed samples taken from the infected patients.
Writing in Nature, they said their work showed the HIV subtype involved began infecting patients in Libya well before the medical workers arrived in 1998.
"All the lines of scientific evidence point in the same direction"
Dr Tulio de Oliveira, Oxford University
An initial trial condemned the medics to death in 2004, but the Libyan Supreme Court overturned the verdicts, and ordered a retrial.
The defendants are accused of knowingly infecting more than 400 children with HIV in the eastern town of Benghazi.
The medics say that they were tortured into giving false confessions.
The first trial lasted almost six years, and the medics have been in jail since 1999.
They say the children were infected through poor hygiene - and a body of scientific work supports their claims.
History of outbreakThe researchers worked on blood samples collected by a network of European clinical research centres that are involved in treating the infected children.
More information: Original paper: de Oliveira T et al. Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak
News date: 2006-12-06
Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. Gifford R, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme AM, Kellam P, Pillay D; UK Collaborative Group on HIV Drug Resistance, AIDS (2006), 20(11):1521-9.