Summary: There are times when the disk checking utility needs to run before you boot into Windows. Sometimes it seems to get stuck and does so every time.
I have a two year old laptop running Windows XP. I had run "Defrag" and also clicked on the check drive for errors option, which was then scheduled at next restart.
Now this scan program runs every time I start up. How can I shut this off?
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Good news: we can turn it off.
Bad news: it means editing the registry.
The "I'm not so sure" news: you shouldn't have to. It should have turned itself off, and I'm concerned that this might be trying to tell you something.
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Checking your disk for errors requires that the checking utility have exclusive access to the hard disk. That means that even Windows can't be accessing the drive for any reason. If the disk drive you're checking is the drive on which Windows lives, the error check is then "scheduled" to happen automatically the next time you boot, before Windows loads. It looks much like this while it's running:

It should happen once. When the utility completes successfully, it should remove that request to run again on boot up, and then reboot. In other words, the next time you boot, which would be upon completion of the scan, it shouldn't check again.
Before I tell you how to turn it off, I want you to watch it one more time, this time paying particular attention to any error messages that it may produce before it completes. (A digital camera snapshot of the screen, as I've done above, is a great way to preserve the error massages before they disappear as the boot continues.) It's possible that there's an issue preventing the scanner from un-scheduling itself.
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In order to disable the scan we'll be making changes in the Windows registry. Step one should be: back it up. This Microsoft Support article Description of the Microsoft Windows registry includes pointers to the recommended ways of doing so.
The short version, for those who are ready to dive into the registry: we're going to change the value of HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\BootExecute to autocheck autochk *.
Step by step that means:
Start the registry editor by clicking Start, then Run, typing in regedit and pressing OK. The result will be similar to this:

Click on the boxed plus sign [+] in front of HKEY_LOCAL_MACHINE. That will expand and look something like this:

Don't worry if your instance of Regedit already had some of these expanded; it remembers the last setting. Just follow along as if it hadn't been, expanding the nodes that we need if they're not already expanded.
Expand (by clicking the boxed plus sign in front of) SYSTEM
Expand CurrentControlSet
Expand Control
Now click on Session Manager, which is listed underneath Control and you should see something like this:
In the right-hand pane, double click on BootExecute. This contains the instruction that we want to remove. You should get an edit dialog much like this:

The command "autocheck autochk /p \??\C:" is what we want to change.
Change replace the "/p \??\C:" with an asterisk (*). The resulting command, "autocheck autochk *" in the dialog looks like this:

Press OK to dismiss the edit dialog.
Close Registry Editor
Now, on your next boot the disk checker should not run.
I say "should" because there are still things that may cause it to run anyway:
You didn't shut down your machine cleanly. Perhaps your machine crashed or suddenly rebooted. Or perhaps you were in a hurry and turned off the power before Windows said it was safe to do so. In both cases Windows may not have finished updating information on the hard disk on shutdown, so it must check the disk on start up to make sure that everything is ok.
The disk may be failing. It's sometimes the case that a disk drive, as it starts to fail, will do so in a way that causes Windows to notice and run the disk checking utility on start up. It's not common, but it can happen.
Related:
Ask Leo! - How do I fix a cyclic redundancy check error when I try to copy a file?
Ask Leo! - How do I fix a bad sector on my hard drive?
Ask Leo! - Your hard disk is more likely to fail than you think.
Article C2990 - April 9, 2007
I carried out the above as disc check started running every time I re-booted. As far as I can see this is a space between '.... autochk *' and the asterisk. However if I leave a space the other wording pops up again when I re-check the registry so I deleted the space.
This has stopped autocheck from running (thank you!) but when I reboot a blue screen appears saying skipping disk check as disabled. Should that happen?
I assume I can still run it manually?
By the way I'm not very technically minded.
David Bieda
Posted by: David Bieda at September 26, 2008 11:53 AMThe exact wording which now apeears on my screen on re=start is:
'Autocheck programme not found - skipping AUTOCHECK'
Which means my machine is still trying to start autocheck each time it starts.
db
Posted by: David Bieda at September 26, 2008 7:29 PMRan CHKSDK with the (disk):/f option on e partition affected, that cleared the command to run it at startup. It worked I don't know why.
Posted by: robert nagler at December 3, 2008 6:00 AMI need a fix for my c drive. I get a message that comes from the toolbar at the bottom. It says msn.exe-corrupt file. The file directory c: is corrupt and unreadable. Please run the chkdsk utility. I did that and finally found your solution to shut the chkdsk off, I hope it works. My question is how do I now fix that error message. My computer will no longer play video when I am online and I need that for school.
Posted by: Brian at January 22, 2009 12:32 PMI had this autocheck autochk * when I opened register and one of diskkept checking every time
Posted by: Beata at March 8, 2009 7:16 AMi had chkdsk checking every time on boot i came here and did all the steps and got to the edit reg and the bootexecute autocheck already had an * so what do i do not to get it to stop????
Posted by: louise at April 27, 2009 8:07 PMautocheck autochk /r \??\C:
autocheck autochk /r \??\E:
autocheck autochk *
autocheck autochk /k:D *
THE ABOVE IS MY BOOTEXEC. ANY SUGGESTIONS AS TO WHAT TO CHANGE SINCE I HAVE NO COMMAND STRINGS WITH THE /P OPTION? THANK YOU IN ADVANCE
IN METTA
Posted by: Keith Ward at July 18, 2009 1:26 AMAnybody know why when I boot up everytime I get the message, "Checking file system on C: the type of file system is NTFS - the volume is dirty. Chdsk is verifying" and then it goes through stage 1 of 3, stage 2 of 3, and then stage 3 of three checks. It takes several minutes of booting up because of this.
Posted by: Lee Nelson Guptill at November 2, 2009 7:51 AMHi Leo, I carefully read your answer to the question, "How do I keep CHKDSK from running on every start-up?" but none of the answers exactly applied to me. This is what my error says: "Checking file system on C: the type of file system is NTFS - the volume is dirty. Chdsk is verifying" and then it goes through stage 1 of 3, stage 2 of 3, and then stage 3 of three checks." Naturally, it takes longer than average to boot up.
Just wanted you to know that I seriously tried and am not being lazy 'cuz I know you are a busy man.
Posted by: Lee Nelson Guptill at November 3, 2009 8:59 AMLeo, you are a 'God Send'......I have been struggling for weeks with this issue and have googled many a site to find the solution and then I found this answer and it worked. It simply worked. Thanks for your clear and consise answer, I was able to have my computer (once again) start without going through the CHKDSK check every time I started it up.....thanks. For a (relative)newbie it was so simple and easy to follow.....thanks a million.
Thanks again for all your help
Harry (Northern Ireland)
Posted by: Harry at November 12, 2009 1:09 AM