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Russia will be the elephant in the room as Pope Francis begins a four-day visit to the Baltics amid renewed alarm about Moscow's intentions in the region it has twice occupied.

Francis boarded a special Alitalia flight that lands early Saturday in Vilnius, the Lithuanian capital, for a four-day trip that also takes in Latvia and Estonia to mark the 100th anniversaries of their independence and to encourage the faith in the Baltic nations, which saw five decades of Soviet-imposed religious repression and state-sponsored atheism.

"Fifty years of occupation left their mark both on the church and on the people," said Monsignor Gintaras Grusas, archbishop of Vilnius. "People have deep wounds from that period that take time to heal."

The trip will feature encounters with political leaders as well as the Catholic, Lutheran and Russian Orthodox faithful.

Grusas notes that all three denominations suffered during communist rule but said those persecutions strengthened their bonds.

"At the time there was this ecumenism of suffering, this ecumenism of martyrdom which Francis speaks about," he said. "There is that closeness."

The three countries, which each have ethnic Russian minorities, are also in lockstep in sounding alarms about Moscow's military maneuvers in the Baltic Sea area following Russia's 2014 annexation of Ukraine's Crimean Peninsula and its support of separatists fighting the Ukrainian government in eastern Ukraine.

The Vatican, however, has been loath to openly criticize Moscow or its powerful Orthodox Church. While seeking to avoid offense, Francis will likely praise the sacrifices of those who fought for independence a century ago during Russia's revolution, and suffered again during Soviet rule.

"The pope will send a message to the world that the difficult history has not been forgotten and that it cannot repeat itself," Lithuanian President Dalia Grybauskaite told the Baltic News Service.

Of the three countries Francis will visit, only Lithuania is majority Catholic, with about 80 percent of its population practicing the faith.

Latvia's population of some 2 million is 25 percent Lutheran, 19 percent Russian Orthodox and only about 16 percent Catholic. Estonia, meanwhile, is often considered one of the world's most non-religious countries. A whopping 76 percent of Estonians profess no religious beliefs whatsoever and Catholics number only 6,000.

The Baltic countries declared their independence in 1918 but were incorporated into the Soviet Union in 1940 and remained part of it until the early 1990s, except for the 1941-1944 Nazi occupation during World War II. All three joined the European Union and NATO in 2004 and are strong backers of the military alliance, which sees them as a bulwark against Russian incursions in Eastern Europe.

The trip, featuring Francis' fondness for countries on the periphery, will be a welcome break for the Argentine pope. His credibility has taken a blow recently following missteps on the church's priestly sex abuse scandal and recent allegations that he covered up for an American cardinal.

Even before he arrived, his trip sparked controversy with Lithuania's tiny Jewish community, which was nearly wiped out during the Holocaust.

Francis will be visiting Vilnius on the 75th anniversary of the final destruction of the Vilnius Ghetto, on Sept. 23, 1943, when its remaining residents were executed or sent off to concentration camps by the Nazis.

But until Francis' schedule was changed three weeks ago, there were no specific events for him to acknowledge the slaughter of some 90 percent of Lithuania's 250,000 Jews at the hands of Nazi occupiers and complicit Lithuanian partisans — a significant oversight for the leader of the world's 1.2 billion Catholics.

At the last minute, the Vatican added in a visit to the Ghetto, where Francis will pray quietly on the day when the names of Holocaust victims are read out at commemorations across the country.

The Vatican spokesman, Greg Burke, acknowledged the lapse but says the visit to the Ghetto will be significant and an important part of the visit.

Francis will also visit the Museum of Occupations and Freedom Fights, located in a former gymnasium that served as the headquarters of the Gestapo during the 1941-1944 Nazi occupation and later as the headquarters of the feared KGB spy agency when the Soviets recaptured the country.

The issue of Lithuanian complicity in Nazi war crimes is sensitive here, with the Jewish community campaigning to have street signs named for heroes who fought the Soviets removed because of their roles in the executions of Jews.

"I think the presence of the pope is showing attention to the Holocaust and to the Holocaust victims," said Simonas Gurevichius, chairman of the Vilnius Jewish Community. "However, it is not the pope who has to do the work, it is Lithuania as a country and as a society who needs to do the work."

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Winfield reported from Vatican City.