Yes. If an instrumental version of a song is being placed in film/TV/advertising or being promoted as a separate work, it's a good idea to register it as a separate version and include ISRC information. 

It's also a good idea to register the instrumental as a separate version if you'd like the splits to be different than on the version with lyrics (i.e. one writer worked on the music and one worked on the lyrics and melody, and you'd like to give the writer who worked on the music 100% ownership of the instrumental).

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