The deal will allow the online store to offer 16 Lennon solo albums which were distributed through EMI Music.
"John Lennon is one of the greatest artists of our time," said Apple chief executive Steve Jobs.
"We are thrilled to have his solo catalogue available on the iTunes Store for the first time."
The albums are distributed through EMI, and will therefore be available to users as iTunes Plus tracks without DRM software and at a higher bitrate. Individual songs will cost 99c, while iTunes Plus songs will cost $1.29.
The deal marks the second time since May that Apple has secured the rights to sell music from a former Beatle. Earlier this year the company cut a deal to sell solo works by Sir Paul McCartney.
McCartney and Lennon's estate control portions of Apple Corporation, the record label which controls The Beatles catalogue.
When Apple Inc launched its iTunes store in 2003, Apple Corporation kicked off a trademark infringement campaign that ran until February 2007.
Rumours of a deal to bring The Beatles catalogue to iTunes have persisted since that time, although no formal deal has been announced.
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