ROME — Pope Francis is heading to the Baltic countries this weekend amid renewed alarm about Russia’s intentions in the region it twice occupied for decades.

Francis’ 25th foreign visit comes a quarter of a century after St. John Paul II made the first papal visit to the former Soviet Union and cheered as Lithuania, Latvia and Estonia emerged from five decades of Soviet-imposed religious repression and state-sponsored atheism.

Hopes were high back in 1993 — the last Russian troops had withdrawn from Lithuania just days before John Paul arrived. There is no such optimism for Francis’ Sept. 22-25 visit.

The three countries, which each have ethnic Russian minorities, are 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.

Russia will be something of the elephant in the sacristy, however, given how the Vatican 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.

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.

Evelyn Kaldoja, head of the foreign desk at Estonia’s largest newspaper Postimees, said history will clearly be front and center during Francis’ visit, his first to the region.

“He really comes to congratulate our countries on the 100th anniversaries of our independence,” Kaldoja said. “And he is expected to show profound respect for the struggle we’ve had to restore our freedom.”

The trip, featuring Francis’ fondness for countries on the periphery, and ecumenical events with Lutheran and Russian Orthodox faithful 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.

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 trip has already sparked controversy with Lithuania’s tiny Jewish community, which was nearly wiped out during the Holocaust.

Francis will be visiting the Lithuanian capital of 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.

Lithuanian and Italian Jewish communities had asked Francis to also visit the official Paneriai Holocaust Memorial, in the forests 11 miles outside Vilnius, where many of the capital’s Jews were executed.

“We wrote many letters and tried many ways, but seems that this is not possible,” Lithuania’s Jewish community leader, Faina Kukliansky, told The Associated Press.

The Vatican spokesman, Greg Burke, acknowledged the lapse.

“We realized it would have been a gap not to do it, especially on this day,” he told reporters. But he said the prayer in the Ghetto would be a “significant” and “important” part of the pope’s Baltic visit.

Francis will also visit the Museum of Occupations and Freedom Fights, located in a former gymnasium that served as both 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.

Monika Garbaciauskaite Budriene, the director of Lithuania’s National TV, said the visit to the museum will send a message to Moscow.

“This will be a tribute to the victims of the KGB, to our painful history and also a signal to Russia and the world that Soviet crimes can not be forgotten or washed away,” she wrote on Facebook.

Dapkus reported from Vilnius, Lithuania. Jari Tanner in Tallinn, Estonia contributed.