In the slums of those two cities, one would be hard pressed to locate a Catholic house of worship, whereas raucous Pentecostal churches holding daily services are numerous.
Yet in recent years, even the Pentecostals are losing steam in Brazil.
"The biggest challenge facing the church in Latin America isn't the growth of the Pentecostals, but the abandonment of a considerable amount of Catholics and others to agnosticism," said Fernando Altemeyer, a theologian at the Catholic University of Sao Paulo.
The church under Francis also must recover from the financial and sexual abuse scandals that marked Benedict's eight-year papacy before he resigned last month.
"The question is whether the new Pope will achieve transparency when managing the church, whether he manages to re-legitimize the moral and financial questions, I think this is key, not only for Latin America but more generally," said Franklin Ramirez of the Latin American Faculty of Social Sciences in Ecuador.
As a cardinal, Pope Francis never held a top post inside the Vatican administration, or curia. This outsider status could pose obstacles in attempts to reform the Vatican, which has been hit with embarrassing disclosures from leaked documents alleging financial cover-ups and internal feuds.
His biographer, Sergio Rubin, told the AP that the new pope reacted strongly to the pedophilia scandal, which hit Argentina among other Latin American countries, saying the church has to make sure that its next priests aren't so susceptible. Only 40 percent of those who enter seminary make it as priests.
"He imposed a system of very strict controls," Rubin said.
The region that celebrated its native son on Wednesday believes he is up to the task.
Jesuits have the gift of spreading the word of God in the most inhospitable of places, said Maurizzio Pavia, an Argentine tourism official who promotes religious and cultural events in Puerto Rico.
"I think his emphasis will be on helping people recover the confidence they had in the church as an institution and as the evangelical messenger," Pavia said.
Associated Press writers Michael Warren in Argentina, Gonzalo Solano in Ecuador, Bradley Brooks and Marco Sibaja in Brazil, Marcos Aleman in El Salvador, Danica Coto in Puerto Rico, and Olga R. Rodriguez and Adriana Gomez Licon in Mexico contributed to this report.
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