After taking negotiations to the brink, the European Union this week agreed — as promised — to open talks with Turkey on its membership in the union. The last-minute decision is typical of EU behavior these days, but Ankara’s accession raises fundamental questions about the EU. This week’s agreement prevents one crisis, but the questions persist. They demand answers and difficult choices for all Europeans.

Turkey and the EU have eyed each other — often warily — for more than 40 years; it became an associate member in 1963. Last December, EU members agreed to open talks with Ankara over membership on Oct. 3. Since then, the union has sustained a series of setbacks, such as the rejection of the EU constitution by founding members France and the Netherlands, and the failure to agree on a budget. In the runup to the commencement of negotiations with Turkey, Austria had become increasingly vocal in its opposition to Ankara’s membership, arguing that the EU was not prepared and demanding progress on Croatia’s bid to join the union as well.

After tense negotiations, both objections were overcome. Austria softened when its opposition isolated it among member states, and the final agreement adopted language that acknowledged that due attention had to be paid to the EU’s “absorptive capacity.” Croatia’s ambitions were advanced when war crimes prosecutors informed EU negotiators that Zagreb had assisted their efforts to bring war criminals to justice.

While the agreement specifies that the goal of the talks is full membership, that is not guaranteed. It is anticipated that negotiations will take at least 10 years, and Turkey must prove to the other members that it has adopted EU laws, regulations and values. Ankara’s human-rights practices, its political system and its treatment of Kurds have all raised questions about its ability to fully join the union. Now, it must, in the words of one EU official, “win the hearts and minds of the European people.”

That process has already begun. Successive Turkish governments have worked to implement the rule of law, move toward a market economy, and eliminate human-rights abuses. Last December’s decision to begin membership negotiations was an acknowledgment of the progress that has been made.

Doubts remain, however, and they do not just reflect concerns about the steps Ankara is taking. Rather, two distinct fears remain: The first is practical. EU expansion from 15 members to 25 has severely taxed the organization. The inclusion of Turkey’s 70 million citizens would greatly magnify the EU’s growing pains. If present trends continue, Turkey would overtake Germany as the union’s largest member, radically altering, if not transforming, the EU decision-making structure.

This in turn raises the second problem: whether Turkey, a Muslim country, is compatible with the values of the predominantly Judeo-Christian members of the EU. Last week, Turkish Prime Minister Recep Tayyip Erdogan stated the issue bluntly: “If the EU wants to become a global power, if it aims to eliminate the conflict of civilizations, the concert of civilizations must be achieved.” The alternative, he said, was that the EU remain a “Christian club.”

Mr. Erdogan is right. Turkey’s membership is crucial for the EU. A failure to honor its commitment to Ankara could have been a final, fatal blow to EU credibility after the battering it took this year. More important, though, the inclusion of Turkey serves strategic purposes. Turkey makes the EU a natural partner for the Middle East, serving as a bridge to vital economic and security interests. It would give the union credibility when engaging the Muslim world. It could help spread democracy and help stabilize an embattled region.

Of course, this assumes the membership bid goes forward. According to some polls, as many as 50 percent of Europeans oppose Turkish membership, for both practical and philosophical reasons. In addition to concerns already cited, some fear a flood of Muslim immigrants. And the EU’s seeming reluctance to engage has soured some Turks on the EU: 60,000 of them took to the streets to protest the EU’s behavior. While a majority still favor membership, the figure has dropped and anger could grow.

Another concern is Turkey’s ability to comply with EU regulations, which must be ratified — or vetoed — by all other EU members. Ankara does not recognize Cyprus, another EU member. That could ultimately jeopardize its bid.

These problems can be resolved. Indeed, they should be. Turkish membership will strain the EU, but the alternative is much worse: an aggrieved nation on the periphery of Europe, whose policies will be based — quite rightly — on the assumption that it is fundamentally alien to European values. That is a recipe for conflict and a genuine clash of civilizations.

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