Repair System Files in Windows Server 2003 Easily (3 Ways)

You will learn 3 helpful ways to repair system files in Windows Server 2003 and how to protect your system files in a better way.


by Delia Updated on May 9, 2024

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The case: system files in Windows Server 2003 corrupted 

"My Windows Server 2003 fails to start because of system files damage! How to repair Windows Server 2003 when system files are corrupted? Do I just need to boot with Windows Server 2003 CD and choose Repair your computer?"

Repair System Files Windows Server 2003

How to repair Windows Server 2003 system files

A system file in computers is a critical computer file. Without it, a computer may not operate correctly. These files may come as part of the operating system, a third-party device driver or other sources. And it’s located in a system folder that cannot be deleted even through the use of permissions. 

However, these system files also may be damaged for some reasons such as viruses or bad sectors. If your system files were damaged and your Windows Server fails to start, you could try the methods below to repair your system files.

Method 1: Use Expand.exe at a command prompt

1. Insert your Windows Server 2003 installation disc into your CD/DVD drive. Change the boot order in BIOS, and press F10 to save changes and restart your computer.

2. When the message “press any key to start from CD or DVD” shows up, press a key and Windows Setup screen will pop out.

Press Any Key

3. Select language and other preferences, and click “Next”.

4. Click “Repair your computer”.

5. Click the operating system that you want to repair and click “Next”.

6. Click “Command prompt” in the System Recovery Options page.

8. Type: expand -r and press Enter. Where is the path to the file that you want to expand on the Windows Server 2003 installation disk, and is the path to save the file.

EXAMPLE: expand –r D:\i386\sfc.dl_ %systemroot%\system32

Command Prompt 1

Method 2: Use the System File Checker tool

1. Enter Command prompt as shown in the above method.

2. Type “sfc/scannow” in the command window and press Enter.

Command Prompt 2

3. Then, the system will automatically scan the integrity of all protected system files and repair the incorrect one by itself.

Method 3: Check and fix the system boot record

1. Enter Command prompt as shown in the first method.

2. Input the following commands in turn and press enter after each to run Windows Server 2003 boot repair:

  • bootrec /fixmbr

  • bootrec /fixboot

  • bootrec /rebuildbcd

Bootrec Command

3. After the scanning and repair process is finished, you can restart your computer to see if you could enter the desktop successfully.

How to protect your Windows Server 2003 system files

System files damage may cause system crash sometimes and the data on the system partition, thereby you have to reinstall your system to make it bootable again. It's complicated and time-consuming. And the data loss is irreversible. 

But you can easily avoid these headaches if you have created a system backup in advance. If not, you can create one after fixing Windows Server 2003 system files corrupted issue. You need a reliable server backup software, AOMEI Backupper Server, for example. And you can benefit from the following advantages: 

Simple and easy to operate: This software has a clear interface and it will select all the boot partitions required to start Windows, you only need to choose System Backup as backup type and the destination path.
Free up your hand: It supports Daily/Weekly/Monthly backup, Event trigger or USB plug in, thus you can backup system automatically without worry about data loss due to no backup or forgetting to backup.
Save disk space issue effectively: By default, it backs up only changed files (using Incremental Backup) and used sectors of file system and compress backup image with normal compression. And it will split backup image size to smaller one automatically. In addition, you can overwrite old backups by deleting it to solve disk space issues completely.

Now, download AOMEI Backupper, install and launch it for system and data protection. For advanced users, try AOMEI Backupper TechPlus (support unlimited PCs & servers).

Download Free Trial Windows Server & PC
Secure Download

1. Select the "System Backup" option under the "Backup" tab. The software will automatically select system and boot related partitions for you.

System Backup

2. Here, you just need to select a destination path to store system image. You can choose to backup system to external hard drive, network, USB, etc.

Select Backup Destination

3. Finally, click the "Start Backup" button to run the backup.

Start Backup

Waiting for the backup task completes, you will have an exact copy of your system partition. But if you want to include changes made later, you need to enable "Schedule Backup" feature before clicking Start Backup.

Click on "Schedule Backup" and then "Enable Schedule Backup", select select Daily/Weekly/Monthly/Event triggers/USB plug in schedule modes in the pop-up window.

Schedule Settings General

As time goes by, this software will create multiple backups and this may result in backup disk full issue sooner or later. To get to the root of this problem, the best way is to delete old backup image with cleanup methods in Backup Scheme. Also, you can change the default backup method to Differential Backup, which backup only changed files since last full backup. 

Click on "Backup Scheme" > “Enable Automatic Backup Cleanup”, and select By quantity, By time, By daily/weekly/monthly cleanup methods. 

Backup Scheme

After creating a system backup, you can choose to create a recovery environment on your server in advance. With this tool, you can restore an image file without booting Windows.


You could try to repair system files in Windows Server 2003 using the above three methods, but there is no guarantee of success. If you could not repair it successfully, your computer may crash and bring you a lot of problems like reinstalling and data loss.

Actually, backing up your system with AOMEI Backupper is an effective way to protect your computer. Furthermore, you can also use it to backup disks and specific files. Moreover, AOMEI Backupper Server supports all the other server systems like Server 2022/2019/2016. You may use it to create Server 2019 bootable disk if needed. Go for it right now!

Delia · Editor
Delia owns extensive experience in writing technology-related blog posts, and has been a part of AOMEI since 2020 to provide expertise in data security and disaster recovery. She works with Windows operating systems, SQL databases, and virtualization platforms such as VMware and Hyper-V, specializing in troubleshooting and advising on data protection and migration.