Pressing topics, such as human rights abuses and the conflict in the Darfur region of Sudan, are to be discussed.
"We will have a frank and open political dialogue where there are no taboos, no sacred cows," said Socrates, whose country currently holds the EU presidency.
The summit is only the second after a meeting in Cairo, the Egyptian capital, in 2000.'Unhappy relations'
John Kufuor, the president of Ghana, and the current chair of the AU, acknowledged that history divided the two continents.
|Britain is not attending the summit|
due to Mugabe's presence [AFP]
He said: "For almost 500 years the relationship between our two continents has not been a happy one."
"The real significance of the summit must be to lay the new foundations of a new partnership of mutual respect."
While the EU wants the summit to open a new chapter in relations, they are struggling to escape the burden of history with Muammar Gaddafi, the president of Libya, calling on Friday for compensation for the colonial era.
El Fassi Abbas, the prime minister of Morocco, said: "The Africa continent has many problems of development, particularly under-development, which have historical causes, in particular colonialism."
Mugabe in focus
The summit marks a return to the European stage for Mugabe, once banned from the EU for allegedly rigging his 2002 re-election, and whose presence has prompted Britain to keep its ministers at home.
Angela Merkel, the German chancellor, challenged European and African leaders on Saturday to confront human rights abuses in Zimbabwe, putting Mugabe in the spotlight at the summit.
Addressing the meeting, Merkel said the world could not stand by while human rights were "trampled underfoot."
"I appreciate that some African states have tried to solve the crisis in Zimbabwe but time is running out.
"The situation of Zimbabwe is damaging the image of the new Africa".
Merkel called on European and African leaders to stand by the people of Zimbabwe and work to promote democracy there.
While a debate on human rights is likely to dominate headlines, the stickiest issue could be over trade where Europe has failed to persuade many African countries to sign up to new pacts once existing agreements expire at the end of the year.
Europe still remains a major market for African goods, but China's presence in the resource-rich continent is growing by the day as it seeks the raw materials needed to fuel its economic growth.
Aid and investment from China, which rarely come with strings attached, have been gratefully received by some African countries which are often frustrated by the conditions that accompany European aid packages.