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/F Fixes errors on the disk.
/R Locates bad sectors and recovers readable information (implies /F).

(from dir /?)

It just sounds like the same thing to me. I never know which one to use - is there even a difference? Or is it maybe for backwards compatibility with previous versions of Windows where there was a difference?

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Using "/F" only takes minutes and using "/R" takes hours ;) – Robert Jul 29 '11 at 11:28
up vote 26 down vote accepted

chkdsk /r does the same thing as chkdsk /f only it also checks for bad sectors on the disk and recovers any readable information. Running chkdsk /r implies that also chkdsk /f is run.

chkdsk /f only checks for disk errors, not bad sectors.

Microsoft has a detailed page for chkdsk. The following is a snippet explaining /f and /r parameters.

Fixing disk errors:

Chkdsk corrects disk errors only if you specify the /f command-line option. Chkdsk must be able to lock the drive to correct errors. Because repairs usually change a disk's file allocation table and sometimes cause a loss of data, chkdsk sends a confirmation message.

Finding physical disk errors:

Use the /r command-line option to find physical disk errors in the file system.

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I have to be honest, I really didn't know that. So /r does a "physical" check on top of what's normally checked by /f. Clear as day now, thanks. – Kez Jul 28 '11 at 7:17
@kez: Exactly. You're welcome. – Mehper C. Palavuzlar Jul 28 '11 at 7:20

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