The pontiff will spend two days in predominantly Catholic Lithuania before moving on to Latvia and then Estonia.
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He was greeted at Vilnius airport by Lithuanian President Dalia Grybauskaite, a military brass band and a group of children waving Vatican flags and singing songs.
He then left for the presidential palace in central Vilnius to make his first address.
The trip is the first by a pope to Lithuania, Latvia and Estonia since 1993. A quarter of a century later, the countries are members of NATO and the euro zone but the past still looms large in a region subject in turn to Soviet and Nazi oppression and where religious persecution left a traumatic legacy.
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In Lithuania, Francis will visit the Vilnius Museum of Occupations and Freedom Fights, a former Soviet KGB prison where hundreds were murdered and thousands shipped off to Siberia, including many priests.
He will also pray at a monument to the victims of the Vilnius ghetto, in a country where only several hundred of over 200,000 Jews survived the Holocaust.
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