They hope to secure the return of five Bulgarian nurses and the Palestinian doctor to complete their life sentences in Bulgaria.
A commission statement said: "The European Commission hopes that this situation, which is so painful and has lasted so long, can be resolved in a humane spirit."
Last week, Libya's Higher Judicial Council commuted death sentences on the six, accused of deliberately infecting 460 children at Benghazi hospital, to life imprisonment.
That opened the way for them to return to their home country under a 1984 prisoner exchange agreement.
Bulgaria and its allies in the 27-member bloc say the nurses are innocent, but have provided long-term medical assistance to victims and aid for the Benghazi hospital.
Families of the HIV victims received payments of hundreds of millions of dollars last week from a compensation fund set up by the Gaddafi Foundation. Once they are sent to Bulgaria, the medics could be pardoned by the new EU member state's president.
Negotiations
Emmanuel Altit, one of three French lawyers representing the Bulgarian nurses, welcomed the visit.
"These are useful discussions and we hope a great deal will come from these discussions," Altit said.
Last Friday, the EU held out the possibility of a boost to relations with Libya if the fate of the medics is resolved satisfactorily.
Some EU officials had voiced private exasperation at what they saw as the new French leader seeking credit for the release of the medics at the last minute after Brussels has spent three years patiently negotiating with Tripoli.
Sarkozy himself is due to visit Libya on Wednesday.