The parents of a British girl who disappeared 20 days ago during family vacation in Portugal prayed for her safe return at the main holy site Wednesday.
Like the shrine at Lourdes, France, Fatima's main church and chapels attract an estimated 6 million pilgrims from around the world each year.
The McCanns' 4-year-old daughter Madeleine disappeared May 3 after they left her and her brother and sister, both aged 2, alone in their room while they went to a restaurant inside their hotel complex in Portugal's Algarve region.
Television pictures showed the McCanns lighting candles and praying privately at a chapel. Other people visiting the shrine kissed them on the cheek, shook their hands and wished them well. The McCanns were due to return to the Algarve later Wednesday.
The late Pope John Paul II visited the shrine twice. He credited the Virgin of Fatima with saving his life after he was shot by a Turkish gunman in St. Peter's Square in 1981.
Meanwhile, a senior official said forensic tests on evidence gathered in the case are still far from being completed.
The head of the National Forensic Medicine Institute, Duarte Nuno Vieira, denied media reports that tests on hair, fiber and sweat samples taken from the hotel room where Madeleine disappeared had yielded no clues.
"The analyses are ongoing," Vieira told Lisbon radio station TSF. "They're far from over, and we'll only be able to draw conclusions once they're completed. ... Things don't go as fast as they do on television."
Police say they have only one formal suspect in the case, 33-year-old Robert Murat, a British man who lives close to the McCanns' hotel in Praia da Luz, about 200 kilometers (120 miles) south of Lisbon.
Police questioned Murat but later released him, saying they did not have enough evidence to bring charges.
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