Check Disk (CHKDSK) is a program for detecting and repairing corruptions of the file system (NTFS, FAT32, etc)
System File Checker (SFC) is a program for detecting and repairing corruptions in the protected system files of the Windows operating system.
As for when to run them - run them when you suspect file system or system file corruptions.
I would first suggest running them in their non-invasive mode. Then examine the output to determine if you need to run it in "fixing" mode
And I agree with MDD1963 - first fix any malware problems BEFORE running them.
For Check Disk, run "chkdsk" (without the quotes) from an elevated (Run as administrator) Command Prompt.
If corruption is detected, run "chkdsk /r /f" (without the quotes) to repair problems that were found
Some will disagree with my inclusion of the "/r" - but the /r isn't documented in current builds of chkdsk (AFAIK), yet I've been using it for years without problem.
For the System File Checker, run "sfc /VERIFYONLY" (without the quotes) from an elevated (Run as administrator) Command Prompt
If corruption is detected, run "sfc /SCANNOW" (without the quotes) to repair problems that were found.
As an aside - CHKDSK and SFC can both show no problems if run on a hard drive that is having physical problems (such as a failing hard drive)
So, it's not a reliable diagnostic tool for a failing hard drive - only use the manufacturer's hard drive diagnostics for that.
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