By Delia / Last update December 13, 2021

The case

"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?"

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


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. Then, you have to reinstall your system. Therefore, you’d better create a system backup in advance. With a system backup image in hand, you can restore it easily without losing data and reinstalling system.

To backup your system, a reliable software like AOMEI Backupper Server is necessary. It is a professional backup software that can help you backup system with only a few steps. And you could backup system to other destinations such as external hard drive, network, USB, etc. In addition, there are many useful features that can save you much time and effort.

Now, download AOMEI Backupper, install and launch it. Then, follow the detailed steps below to backup your Windows Server 2003 system files.

Download Free Trial Windows Server & PC
Secure Download

1. Select the "System Backup" option under the "Backup" tab.

System Backup

2. The software will automatically select system and boot related partitions for you. Here, you just need to select a destination path to store system image.

Select Backup Destination

3. (Optional) You may configure backup schedule and scheme based on your needs.

a) You can click on “Schedule Backup” to select Daily/Weekly/Monthly/Event triggers/USB plug schedule modes in the pop-up window.

Schedule Settings General

b) You can click on "Backup Scheme" > “Enable Automatic Backup Cleanup” to select one kind of deletion mechanism to delete old backup images automatically. You can also change the backup method as per your need.

Backup Scheme

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

Start Backup


You could try to repair system files in Windows Server 2003 using 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!