|Japa is the repetition of a mantra. This is done by counting the beads of a rosary (Japa-mala) or the divisions of fingers.
There are three kinds of japa.
1. mantra is audibly repeated
2. There is no audible sound, but only the movements of lips, and
3. Repetition is purely mental.
Gita says that of all yajnas (sacrifices) japa-yajna is the highest. In other yajnas a man sacrifices something else, but in japa-yajna he sacrifices his own self and becomes the self of-the Devata whom he worships.
Source : http://hindubooks.org/essence_of_hinduism/hindu_rituals_and_myths
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