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As @Gilles says, since du counts only the first of all hardlinks pointing to the same inode it encounters, you can give it directories in a row: $ du -hc --max-depth=0 dirA dirB 29G /hourly.1 1G /hourly.2 30G total I.e. any file in 'hourly.2' referencing an inode (aka "real" file) already referenced in 'hourly.1', will not be counted.

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