How to set up a clean boot configuration using msconfig

In a clean boot configuration the usual start-up programs do not start, and non-Microsoft services are not started. This configuration is most easily set up with the aid of msconfig. (Windows 2000 does not come with msconfig. You can download it here.) In a clean boot many problems may disappear, at least as long as you stay in this configuration. If your computer does not boot to the Desktop in normal mode, but you can boot to safe mode, you may be able to get back to normal mode in a clean boot. Likewise, if you cannot connect to your local network or the Internet, you may find connectivity restored in clean boot. A clean boot may also keep some (but unfortunately not nearly all) viruses, worms, spyware and ad-ware from starting, thus giving you a better chance at removing them. Clean boot is also the second step in clean boot troubleshooting (also known as safe mode troubleshooting,) a fundamental and frequently used troubleshooting procedure in later versions of Windows. The discussion here applies to setting up a clean boot configuration in Windows 2000, Windows XP, Windows 2003 and Windows Vista.

Note: msconfig makes changes to the registry when you select Apply and when you exit. If a security program running in the background notifies you that registry changes are being made, and asks you whether to allow them, you must allow the changes!

To set up a clean boot configuration with msconfig:

Windows Vista

Go to Start, select All Programs, then Accessories and finally select select Run. In the Run box type "msconfig" (without the quotes) and hit Enter on your keyboard or click OK. If you are prompted for an administrator password or confirmation, type the password or provide confirmation.
In the System Configuration Utility, on the General tab select Selective Startup. Then click the three checkboxes below Selective Startup to uncheck them. (Leave Use Original BOOT.INI selected.)

Windows XP, 2000

Go to Start, then select Run. In the Run box type "msconfig" (without the quotes) and hit Enter on your keyboard or click OK.
In the System Configuration Utility, on the General tab select Selective Startup. Then click the four checkboxes below Selective Startup to uncheck them. (Leave Use Original BOOT.INI selected.)

Both

Unchecking one the check boxes on the General page is equivalent to selecting the equivalent tab across the top and then either unchecking all the checkboxes under that tab, or selecting Disable All. Checking one of these check boxes it equivalent to selecting the equivalent tab across the top and then either checking all the checkboxes under that tab, or selecting Enable All. If under the tab in question there are both checked and unchecked checkboxes, then the checkbox on the General tab corresponding to this tab will be tri-state, or gray-filled.

Click Apply. Next click OK or Close. When you are asked whether you want to Restart or Exit without restart, click Restart. Your computer will shutdown and restart.
Msconfig does not actually "enable" or "disable" things in a literal sense. What is does is remove the registry settings that Windows reads to determine which services or programs to start when starting up the computer or logging on a user. Therefore the changes you make in msconfig do not take effect until you reboot your computer.
Upon reboot and after logging in, a window will pop up notifying you that msconfig is in selective startup.
In Windows Vista a balloon in the notification area may notify you that Windows has blocked some startup programs. Click on the indicated icon in the notification area, select Run blocked program and then select System Configuration Utility. In the User Account Control window click Continue.

Click OK to close the window notifying you that msconfig is in selective startup. Msconfig will open. You may close it if you wish. If you are asked whether you want to restart or exit without restart, click Exit without restart.

You may find that on the General tab the Load Startup Items checkbox is no longer unchecked, but gray, or "tri-state." Some programs check to determine that they have been disabled, and re-enable themselves. For the moment ignore these programs, but if the problem you are investigating persists and you suspect one of these programs is causing it, then you will have to open the program and see is you can find a properties or other setting to prevent is from loading automatically when the computer starts, or else uninstall the program.
When you are through, return msconfig to normal startup. Once again, to Start, select Run and type "msconfig" (without the quotes) and hit Enter on your keyboard or click OK. In the System Configuration Utility, on the General tab click Selective Startup to choose it. Click Apply, then OK or Close. When you are asked whether you want to Restart or Exit without restart, click Restart. Your computer will shutdown and restart to a normal boot configuration.

Never leave msconfig in a selective startup configuration longer than you need for your troubleshooting session. Changes made with msconfig should only be temporary. Some users use msconfig to permanently prevent programs from starting up, but this is not a good practice. For instance, if you uninstall a program while it is disabled in msconfig, the uninstall routine will not find the startup entry in the registry, as msconfig has removed it. If you return msconfig to a normal startup, or even just recheck the program in the Startup tab, msconfig will return the registry key to its original value, and on the next startup the program will not be found, having been uninstalled. Windows will then issue a warning message that a file was not found. The preferred means of stopping programs from starting is to examine the preferences or options of the program, and stop it from starting using the program's preferences. If it is a program you don't use, it might be a better idea to use Add or Remove Programs to uninstall it.