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The answer is "NO". When you attempt encrypt a system database, SQL Server complains: Cannot encrypt a system database. Database encryption operations cannot be performed for 'master', 'model', 'tempdb', 'msdb' or 'resource' databases.


Community Wiki answer generated from comments on the question by QueueMann and Aaron Bertrand♦ Database backup files throws away any unused space in your data files in the backup process. TDE doesn't have to encrypt empty pages, and the backup process doesn't have to include the space in the backup, but they are still empty pages contributing to data file ...

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