Windows\System32\config\SYSTEM is missing or corrupt [Fix]

Some Windows may encounter an error where they can not start Windows because an important system file is missing or corrupted. This is the error message you may see:

Windows could not start because the following file is missing or corrupt:

\Windows\System32\config\SYSTEM

Windows failed to load because the system registry file is missing or corrupt.

If you are facing the same error, read the entire article to learn the best possible fixes.

Windows\System32\config\SYSTEM is missing or corrupt

The Windows\System32\config\SYSTEM is missing or corrupt error can occur because of multiple reasons such as missing or corrupted Registry files.

These are the things you can do to fix Windows\System32\config\SYSTEM is missing or corrupt.

Scan Hard Drive and System files
Restore Registry Files
Repair Windows using Installation Media.

Let us talk about them in detail.

Windows failed to load because the system registry file is missing or corrupt

1] Scan Hard Drive and System files

$Fix Windows\System32\config\SYSTEM is missing or corrupt$

Windows\System32\config\SYSTEM is missing or corrupt error can be because of some bad sectors in your Hard Drive. So, the best option is to try and fix these sectors. You can do that pretty simply by starting the computer with Windows ISO Media.

Now, click Repair your computer > Command Prompt, type the following command, and hit Enter.

chkdsk c: /r

Wait for the process to complete, restart your computer and check if the issue persists.

If it doesn’t work, try running SFC, the System File Checker command. In the Command Prompt, type the following command and hit Enter.

sfc /scannow

Wait for the process to complete, restart your computer and check if the issue persists.

2] Restore Registry

The problem can be caused by Registry files. If they are missing or corrupted, we need to restore them to fix the issue.

So, launch Command Prompt (as we did in Solution 2) and type the following commands to backup your Registry, in case if something goes wrong.

md tmp

copy c:\windows\system32\config\system c:\windows\tmp\system.bak

copy c:\windows\system32\config\software c:\windows\tmp\software.bak

copy c:\windows\system32\config\sam c:\windows\tmp\sam.bak

copy c:\windows\system32\config\security c:\windows\tmp\security.bak

copy c:\windows\system32\config\default c:\windows\tmp\default.bak

Now, delete the current Registry files.

delete c:\windows\system32\config\system

delete c:\windows\system32\config\software

delete c:\windows\system32\config\sam

delete c:\windows\system32\config\security

delete c:\windows\system32\config\default

Finally, use the following commands to repair Registry files.

copy c:\windows\repair\system c:\windows\system32\config\system

copy c:\windows\repair\software c:\windows\system32\config\software

copy c:\windows\repair\sam c:\windows\system32\config\sam

copy c:\windows\repair\security c:\windows\system32\config\security

copy c:\windows\repair\default c:\windows\system32\config\default

Note: Replace “C” with the Drive letter in which your OS is stored.

Now, close the Command Prompt and reboot your computer to check if the issue persists.

Useful reads:

3] Repair Windows using Installation Media

If Automatic Startup Repair also does not help, then you need to repair Windows using the Installation Media.

Hopefully, we have helped you to fix Windows\System32\config\SYSTEM is missing or corrupt error.

How to fix System registry file is missing or corrupt?

Use the SFC (System File Checker) and DISM (Deployment Imaging Service Management) commands to fix a missing or corrupt system registry file. Open Command Prompt as an administrator and run sfc /scannow followed by DISM /Online /Cleanup-Image /RestoreHealth. These tools help identify and repair corrupted system files, including registry issues.

What is 0xc00000e9 System registry file is missing?

The 0xc00000e9 error code signifies a hardware issue or corrupted system file during boot, not specifically indicating a missing system registry file. It often points to unexpected I/O errors, which may surface before the Windows login screen. To resolve this, check the hardware connections and use recovery tools to address file corruption.