For those that don’t know, the CHKDSK utility is a way that Windows validates the system file structure and integrity of your computer’s hard drive. You can scan your hard drive with it or run it with a fix (/f) flag to correct issues on your local hard drive.

But, when time is critical, many of us don’t want to wait around while the system is scanned, especially if for some reason, it is happening each and every time you start up. When that happens, you either have a serious problem with your computer, or somehow your system has been automatically set to do this scan.

While we don’t recommend stopping these scans, especially if your system does indeed have problems, having this run every single time you start up borders on maddening! So after some digging, research and testing, we have found the way to prevent (and fix) this from happening.

Prevent CHKDSK from running On Every System Restart

Below are the steps and command you need to do to get this to work. As we mentioned, We tested this on Windows 7 but we believe this will work on Windows XP as well.

The first step is to see if you have a “dirty” hard drive. If this test does say that you do, it could be the reason why you continually see a CHKDSK running on every restart. To test this, you need to launch a Command prompt as the Administrator of your computer.

Go to Windows Button, and type in “cmd” in the “Search for Programs and Files” box.

When the application shows, right-click on it and choose “Run as Administrator”.

Next you will type in the following command to check to see if your hard drive is “dirty” or not:

fsutil dirty query x:

Where “X:” is actually the drive letter of your hard drive (in which resides Windows folder). For us it was “C:” but in this article, we will refer to it as “X:”.

Run the command and if your hard drive is indeed “dirty”, you will see something like this:

If your drive is “not dirty” then you may have something else going on. You might still want to go through the following steps though.

Instruct Windows Not To Scan At Next Reboot

The next thing that you will do is instruct Windows to not execute the CHKDSK command at the next reboot using the CHKNTFS command. To do this, in the command prompt, type in:

chkntfs /x x:

Again, be sure to change the “X:” to whatever drive you are checking.

Now reboot your computer. Hopefully, CHKDSK will not run this time. But you need to go on with the following instructions to ensure your hard drive is ok.

Optional: you might want to run the “dirty” check again. When we did, it still said that ourdrive was dirty.

Instruct Windows To Do a Deep CHKDSK Scan At Next Reboot

We will preface this set of instructions with a warning. This deep CHKDSK scan will take several hours to run. On our 500 GB hard drive, it took over 3 hours to complete, but with success in the end.

What you are going to do here is tell Windows to do a CHKDSK scan but do a very thorough job at it. If you already have your command prompt open (running as Administrator), issue the following command:

chkdsk x: /f /r

Remember to replace the “X:” with the drive letter (Windows volume) of your hard drive.

The /f flag tells windows to fix any issues and the /r flag tells it to do a deep scan. It locates bad sectors and recovers whatever information is readable.

Now, restart your system. When it reboots, it will start the CHKDSK process:

Head off to do something else, hopefully fun, during this time. It will take a long time for this to complete.

Your computer will automatically restart when it is completed. If there are issues, you will see a message on the screen and you may have to do something else or run CHKDSK again.

Once you boot back up into Windows, launch the Command prompt again (as Administrator) and check to see if your hard drive is dirty or not. Here is the result of our check:

The HDD now is no more "dirty". So there you have it. Hopefully this procedure will work for you.