The Pontiff made the plea on Sunday in front of pilgrims at his summer residence in Castel Gandolfo outside Rome.
"In this historic moment, in which we see the important process of European unification through the enlargement of the European Union to other countries, the Church gazes on this continent with a look full of love," the Pope said.
"But amid so much light, there are also shadows," he added.
High-ranking officials from the Church of England and Orthodox churches across Europe, including Greece, Romania and Russia have supported the Pope's call to include a clear reference to Europe's Christian heritage in the draft.
The final draft of the EU constitution is expected to be presented next Friday to Italy's Prime Minister Silvio Berlusconi.
The Italian premier, whose country holds the rotating presidency of the bloc, has said he would seek a compromise on the mention of Christianity.
Valery Giscard D'Estaing, the head of the EU body which hammered out the constitution has defended the absence of the reference.
D'Estaing argued some member states would not have accepted it. But he added the preamble referred to spiritual feelings in Europe which was "an obvious reference" to Christianity.
The constitution is expected to outline the EU's future shape and policies.
It will need the unanimous approval of all member states before the legal document takes effect, expected in 2005.