The EU "has conducted a complete review of the persons and entities subject to the EU’s autonomous regime on specific measures directed against certain persons and entities with a view to combatting terrorism," a statement said.
A total of more than 60 people and groups figure on the blacklist, including the armed Basque separatist group ETA, Sri Lanka’s Tamil Tigers and the Islamist group Hamas.
Those on it are subject to an asset and funding freeze.
The register was drawn up to respect a UN Security Council resolution adopted in the wake of the September 11, 2001 attacks which demanded that countries crack down on "terror" financing.
It is usually revised every six months but this had not happened, until Friday, since before a European court annulled on December 12 the listing of the People’s Mujahedeen of Iran (PMOI) in May 2002.
The Court of First Instance, Europe’s second-highest tribunal, ruled that the EU had not respected the group’s right to a fair hearing.
Under the review, the EU will now provide a "statement of reasons" to all those whose assets are frozen and notify them of their right to ask that the decision to list them be "reconsidered".
A special working group was also set up to study listing and de-listing.
PMOI still figured on the new "terrorist list" published Friday, and the Greek far-left group Revolutionary Struggle was also added to it.
Founded in 1965 with the aim of replacing first the shah and then the clerical regime in Iran, PMOI has in the past operated an army inside Iran.
It was the armed wing of the France-based National Council of Resistance of Iran but it renounced violence in June 2001.
Its exiled leader Maryam Rajavi lives in France and regularly visits Brussels.