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Jolie was given the "Honorary Heart of Sarajevo" award not "only because of her exceptional career in the movie world, but also due to her exceptional engagement in the real world," the festival's director Mirsad Purivatra said at the ceremony.
Purivatra referred to Jolie's activities to help Bosnia's refugees, forced to leave their homes during the bloody 1992-1995 conflict that left 100,000 people dead and almost half of a four-million prewar population displaced.
Jolie, visibly moved by a standing ovation from the audience in the national theatre, broke down in tears as she thanked the organisers stressing she was honoured by being at the festival that was born during Bosnia's war.
"I told Brad in the car I was afraid I was going to cry," the 36-year-old actress, wearing a long peach dress, said.
"It is so wonderful to be here ... we are very honoured to be invited to this festival," Jolie told journalists on the red carpet before entering the theatre in downtown Sarajevo.
"We will be back to the kids tonight, but we will be back" to Sarajevo, she replied when asked how long they were planning to stay in the Bosnian capital.
Hundreds of Sarajevans gathered in the square in front of the theatre and cheered the two actors. The smiling couple posed for photographers and signed autographs for fans.
At one point Jolie approached the crowd to greet a baby being carried by a man.
Organisers of the 17th Sarajevo Film Festival said earlier in a statement that Jolie was their special guest, although the visit was kept secret until the very last moment.
Jolie visited Bosnia twice in 2010 as a UNHCR good will ambassador, meeting some of the refugees.
Last year Jolie filmed her directorial debut, a love story between a Muslim woman and a Serb man set against the background of Bosnia's inter-ethnic war.
"The Land of Blood and Honey" caused controversy in Bosnia when local media speculated that the film was the story of a Muslim rape victim who falls in love with her Serb attacker. The rumours prompted angry reactions from some victims' organisations.
However, Jolie asked the victims to be patient until they see the movie. According to the synopsis, the movie is a wartime love story between a Serb guard in a prison camp and a Muslim detainee, his former girlfriend.
At the SFF closing ceremony the "Heart of Sarajevo" best movie award was given to "Breathing," directorial debut of Austria's actor Karl Markovics.
Thomas Schubert who plays in "Breathing," a drama about a young parolee, received the best actor award while Romania's Ada Condeescu was proclaimed the best actress for her role in "Loverboy."
Born as an act of resistance when the Bosnian capital was under siege during the 1992-1995 war, the Sarajevo Film Festival has become a cutting-edge event where young European talent is revealed.
Besides the official competition for the award for the best movie, 200 films, long and short, were screened at the July 22-30 festival, which has grown to be one of the largest in Europe
