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Francis came from a leading family in Andalusia, Spain. Perhaps it was his popularity as a student that enabled Francis in his teens to stop two duelists. He entered the Friars Minor in 1570, and after ordination enthusiastically sacrificed himself for others. His care for the sick during an epidemic drew so much admiration that he became embarrassed and asked to be sent to the African missions. Instead he was sent to South America in 1589.

While working in what is now Argentina, Bolivia and Paraguay, Francis quickly learned the local languages and was well received by the indigenous peoples. His visits to the sick often included playing a song on his violin.

Around 1601 he was called to Lima, Peru, where he tried to recall the Spanish colonists to their baptismal integrity. Francis also worked to defend the indigenous peoples from oppression. He died in Lima and was canonized in 1726.