Laird writes that Altan Khan abolished the native Mongol practices of shamanism and blood sacrifice, while the Mongol princes and subjects were coerced by Altan to convert to Gelug Buddhism—or face execution if they persisted in their shamanistic ways. Committed to their religious leader, Mongol princes began requesting the Dalai Lama to bestow titles on them, which demonstrated "the unique fusion of religious and political power" wielded by the Dalai Lama, as Laird writes. Kolmaš states that the spiritual and secular Mongol-Tibetan alliance of the 13th century was renewed by this alliance constructed by Altan Khan and Sönam Gyatso. Van Praag writes that this restored the original Mongol patronage of a Tibetan lama and "to this day, Mongolians are among the most devout followers of the Gelugpa and the Dalai Lama." Angela F. Howard writes that this unique relationship not only provided the Dalai Lama and Panchen Lama with religious and political authority in Tibet, but that Altan Khan gained "enormous power among the entire Mongol population."

What practice did Altan Khan put to an end?