Pope John Paul II leaves Thursday for a conference of Latin American bishops in Puebla, Mexico, that represents the greatest challenge so far in his fledgling papacy. It is a trip that could determine the future of the Roman Catholic Church in the troubled Latin region.

This is the first trip abroad as pope for Polish-born John Paul, and is expected to deal with smoldering controversies over the political, social and economic role of the church in an area marked by extremes of wealth and poverty and scarred by political oppression, torture and revolutionary violence.

Today, on the eve of the pope's departure for his first stop, in the Dominican Republic, the Vatican announced that the pontiff will personally mediate a Chilean-Argentine border dispute that has raised fears of war. A papal emissary had laid the groundwork for the pope taking up the mediation between the two rightwing military governments.

The official theme of the two-week Puebla conference, at which the pope will make only a brief appearance, is "evangelization in the present and future of Latin America."

But the real issue, in a region whose population will soon represent more than half of the world's 700 million Catholics, is a choice between more aggressive social involvement by the church or more traditional religious commitment.

The meeting could therefore fuel longstanding conflicts between conservatives and progressives. Many of Latin America's 356 bishops, representing 22 countries, are divided into two theological schools -- those who feel that creating an active Christian society would be sufficient and those who believe that the church must help work toward a profound transformation of contemporary Latin American life.

The ideological content of the pope's speech when he inaugurates the conference at the Shrine of Our Lady of Guadaloupe on Saturday is thus thought likely to significantly influence the course of the conference.

Since John Paul's election in October, he has warned against excessive political involvement by the church as a whole and by individual priests. Over the last three months, however, he has repeatedly stressed the importance of individual rights, which, along with religious freedom, include freedom of speech and freedom from want.

What the pope says in Puebla will have to take into account the fact that in many parts of Latin America, local churches are already embroiled in disputes with some of the area's military governments.

In recent years the episcopates of Chile, Argentina, Brazil, Nicaragua and El Salvador have spoken out forcefully against opression, toture, poverty and exploitation.

John Paul's trip to Mexico for the third Latin American Bishops' conference will mark the second papal visit to Latin America in little more than a decade. In 1968, Pope Paul VI visited Medellin, Colombia, to attend the second conference. The first conference was held in Rio de Janeiro in 1955.

At the Medellin conference, which came one year after Pope Paul's "people's progess" encyclical, the bishops of Latin America broke away from years of identification with the powerful and the landed wealthy and chose dedication to the poor and oppressed of their largely underdeveloped nations.

"The Latin American episcopate cannot remain indifferent to the tremendous social injustices that exist in Latin America and which keep the majority of our peoples in a painful poverty that often approaches levels of inhuman misery," the bishops wrote.

At that time there was great hope for political change, whether of the democratic type then prevailing in Chile, or of the Marxist variety as in Cuba.

Not surprishingly the Medellin shift led to increased church involvement in political affairs, producing in some factions of the church a theology of liberation that others consider far too extreme. It also fostered a plethora of grass-roots Catholic communities that have raised the problem of a "parallel church."

Today, the situation in Latin America has changed, with military and dictatorial governments dominating many countries. There are those who feel that at Puebla there will be a parallel church trend toward the doctrinal and disciplinary orthodoxy to which the new pontiff has already demonstrated his devotion.

The working document that has come out for two years of preparation for the conference demonstrates the problems that will confront both the pope and his bishops in Mexico. In its condemnation of both communism and undiluted capitalism, its concern with downtrodden workers, peasants, and women, frustrated political thinkers, and starving and diseased children, the document confirms the stance taken at Medellin.

When it comes down to operative suggestions for the future, however, there is indecision about the path that the church should follow.