"The Last Jew" by Noah Gordon.
"Set in Spain under the Inquisition, this latest big historical novel from Gordon (Shaman; The Rabbi) follows the adventures of young Yonah Helkias as he stays true to his Jewish faith, escapes from misadventures and finds love. In Toledo, in 1489, a precious reliquary of a Christian saint, crafted by Yonah's silversmith father, disappears; Yonah's older brother, who was delivering the relic, is found dead; and compassionate physician Bernardo Espina begins to investigate the theft and murder. Meanwhile, the Inquisition starts to target Jews, including conversos like Espina (Jews by birth who have entered the Catholic church). The bulk of the novel takes place three years later, when the deadline for all Jews to leave Spain has arrived. Yonah, aged 13, joins thousands of his co-religionists headed for Spanish borders and ports, but instead of departing, Yonah remains behind."
http://www.amazon.com/gp/product/0312300530/sr=8-2/qid=1142127233/ref=pd_bbs_2/102-3484858-4967359?%5Fencoding=UTF8