Startup Error ‘System registry file is missing, or corrupt’ [3 Fixes]

As it turns out, some users are encountering the ‘System Registry File is Missing’ error during the booting procedure. As a result, they are unable to start their computers conventionally. Most affected users are reporting that the error occurs a few seconds after the final loading screen (of the booting procedure) appears. Although this error is mostly reported to occur on Windows 10, we’ve managed to find a lot of instances of it happening on Windows 7 and Windows 8.1 computers.

System Registry File is Missing Startup error on Windows


What’s causing the ‘System Registry File is Missing’ error on Windows?

We investigated this particular issue by looking at various user reports and by testing out the various repair strategies that are recommended by other users that already managed to threat the symptoms of this issue. As it turns out, several different scenarios might lead to the apparition of this issue. Here’s a list of potential culprits that might be responsible for this problem:

  • Wrong startup configuration – If you’ve previously set up a dual boot system, chances are the wrong BCD data is being used during the startup procedure. In this case, you should be able to resolve the issue by booting to the last known good configuration. Several affected users have confirmed that this procedure was effective in their case.
  • Corrupted BCD data – Once of the most common causes that will produce this particular error is an underlying booting problem caused by corruption inside the BCD data. If this scenario is applicable, you should be able to fix the problem by using the Bootrec.exe utility to repair the corrupted BCD data.
  • System file corruption – As it turns out, system file corruption can also be responsible for the apparition of this startup error. Several affected users that were also encountering this issue have managed to fix it by running a couple of utilities capable of fixing system file corruption (DISM and SFC). In most severe cases, you might need to reset every OS component with a repair install or a clean install procedure.

Method 1: Booting to the last good configuration

If the issue only started occurring recently and you’re looking for a fix that doesn’t involve complicated troubleshooting strategies, you should start by seeing if your computer is capable of completing the startup procedure by using the last good configuration.

Several affected users have reported that they finally managed to bypass the startup System Registry File Is Missing error by forcing the Startup options screen to appear and selecting the Last known good configuration from the list.

Here’s a quick guide on booting from the last good configuration:

  1. Start your computer and start pressing F8 repeatedly as soon as you see the initial screen to arrive inside the Advanced Boot Options.
  2. Once you’re inside the Advanced Boot Options screen, select Last Known Good Configuration from the list of available options.
  3. Wait for the procedure to complete and see if the startup procedure completes without issues.

If the same problem is still occurring, move down to the next potential fix below.

Method 2: Fixing the booting sequence

As it turns out, one of the most common instances that will spawn the ‘System Registry File is Missing’ error during the startup sequence is an underlying booting problem. In these cases, the only effective way of getting to the bottom of the issue is to repair the entire booting sequence by using the Bootrec.exe.

Bootrec.exe is a built-in Windows utility capable of fixing the entire master boot record, the whole booting sequence, and the boot configuration data. Keep in mind that any of these components might be responsible for the current error that you’re dealing with.

Prerequisite: Keep in mind that to perform this installation procedure, you need a valid Windows installation media that is compatible with the operating system that you’re using. If you don’t have that already, you can create one by following the instructions outlined in one of the resources featured below:

Note: Choose the article that applies to the operating system that you’re using. And in case you don’t have the installation media and no means of obtaining one, you can force the Startup Recovery menu to appear by forcing 3 consecutive startup interruptions (turning off the computer in the middle of the booting sequence).

Once you have the prerequisite, follow the instructions below to run the Bootrec.exe utility to resolve the ‘System Registry File is Missing’ error:

  1. Start the operation by inserting the installation media before the booting sequence can begin. Next, press any key when prompted to boot from in. Once you see the initial Windows installation window, click on Repair your computer (You can see it either in the bottom right or the bottom left corner, depending on your Windows version).
    Choose Repair your computer
  2. You should be taken directly to the Advanced Options menu. Once you get there, click on Troubleshoot, then select Command Prompt from the list of available options.
    Choosing Command Prompt from Advanced Options
  3. Once you’re inside the elevated Command prompt window, type the following commands inside and press Enter after each command to rebuild the entire Boot Configuration data:
    bootrec.exe /fixmbr
    bootrec.exe /fixboot
    bootrec.exe /scanos
    bootrec.exe /rebuildbcd
  4. Once all commands have been processed successfully, all boot configuration data should be repaired. All you need to do now is test the startup procedure to see if it completes without any errors.

If you’re still encountering the same error during the booting procedure, move down to the next method below.

Method 3: Repairing System File Corruption

As it’s been confirmed by several affected, users the ‘System Registry File is Missing’ error can also be triggered by some degree of System File corruption that is interfering with the booting sequence. Keep in mind that under normal circumstances, you should open an elevated Command prompt to run the two utilities.

But since you can’t get past the booting sequence, you will need to perform these scans before the booting sequence completes. To do this, you’ll need to open up an elevated CMD prompt using the Advanced Options menu.

Here’s a quick guide that will guide you through the procedure of running SFC and DISM scans from a CMD opened from inside the Advanced Options menu:

  1. Start by inserting the installation media and restarting your machine. Before you get to see the first startup screen, start pressing any key to boot from the Windows installation media.
    Press any key to boot from installation media
    Press any key to boot from installation media
  2. Once you find yourself at the initial Windows screen, click on Repair your computer (bottom-left corner of the screen)
    Choosing Repair your computer from Windows Setup
  3. At the next menu, start by selecting the Troubleshooting tab, then click on the Advanced Options. Once you get to that menu, select the Command Prompt options.
    Command Prompt in Advanced options
  4. Once you manage to get inside the elevated Command Prompt, type the following command and press Enter to initiate a System File Checker scan:
    sfc /scannow

    Note: Keep in mind that SFC is using a locally cached copy to replace corrupted files with healthy copies. Interrupting this utility after the initial scan has been started is not recommended since you leave your system exposed to other logical errors. Wait patiently until the procedure is complete.

  5. Once the SFC scan is complete, restart your computer and re-follow the steps above to return to the elevated CMD screen at the next system startup. After you manage to return to the elevated CMD prompt, type the following commands and press Enter after each one to investigate and fix corruption instances using the DISM utility:
    Dism /Online /Cleanup-Image /CheckHealth
    Dism /Online /Cleanup-Image /ScanHealth
    Dism /Online /Cleanup-Image /RestoreHealth

    Note: This utility is highly dependent on the Windows Update component. It uses WU to download healthy copies of the corrupted files that need to be replaced. Because of this fact, make sure that your Internet connection is stable before initiating the DISM scan.

  6. Once the procedure is complete, restart your computer and see if the issue is resolved at the next system startup.

If the same ‘System Registry File is Missing’ error is still occurring during the startup sequence, move down to the next method below.

Method 4: Performing a repair install

If you’ve followed all the potential fixes above and you’re still encountering the same ‘System Registry File is Missing’ error, chances are you’re dealing with an underlying system file corruption issue that cannot be resolved conventionally.

If this scenario is applicable, the only way of resolving the OS-related issues is to follow a procedure that will reset every Windows component. When it comes to achieving this state, you have two ways forward:

A clean install is a more straightforward option that doesn’t require any prerequisites, but the major downside is that you will experience serious data loss – Personal files, applications, user preferences and any other type of data will be lost unless you back it up in advance.

If you want a more efficient approach, go for the repair install procedure. Although it’s a more tedious procedure and it requires you to have a valid Windows installation media, it will only reset your Windows components. But the major advantage is that you will be able to keep all your files (documents, pictures, music, etc.) applications, games, and even some user preferences.


Kevin Arrows

Kevin Arrows is a highly experienced and knowledgeable technology specialist with over a decade of industry experience. He holds a Microsoft Certified Technology Specialist (MCTS) certification and has a deep passion for staying up-to-date on the latest tech developments. Kevin has written extensively on a wide range of tech-related topics, showcasing his expertise and knowledge in areas such as software development, cybersecurity, and cloud computing. His contributions to the tech field have been widely recognized and respected by his peers, and he is highly regarded for his ability to explain complex technical concepts in a clear and concise manner.