Like other files and services in Windows, all registry keys may be restricted by access control lists (ACLs), depending on user privileges, or on security tokens acquired by applications, or on system security policies enforced by the system (these restrictions may be predefined by the system itself, and configured by local system administrators or by domain administrators). Different users, programs, services or remote systems may only see some parts of the hierarchy or distinct hierarchies from the same root keys.

Windows 98 and Windows ME include command line (Scanreg.exe) and GUI (Scanregw.exe) registry checker tools to check and fix the integrity of the registry, create up to five automatic regular backups by default and restore them manually or whenever corruption is detected.[40] The registry checker tool backs up the registry, by default, to %Windir%\Sysbckup Scanreg.exe can also run from MS-DOS.[41]

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With Windows 95, Windows 98, Windows ME and Windows NT 4.0, administrators can use a special file to be merged into the registry, called a policy file (POLICY.POL). The policy file allows administrators to prevent non-administrator users from changing registry settings like, for instance, the security level of Internet Explorer and the desktop background wallpaper. The policy file is primarily used in a business with a large number of computers where the business needs to be protected from rogue or careless users.
.REG files (also known as Registration entries) are text-based human-readable files for exporting and importing portions of the registry. On Windows 2000 and later, they contain the string Windows Registry Editor Version 5.00 at the beginning and are Unicode-based. On Windows 9x and NT 4.0 systems, they contain the string REGEDIT4 and are ANSI-based.[21] Windows 9x format .REG files are compatible with Windows 2000 and later. The Registry Editor on Windows on these systems also supports exporting .REG files in Windows 9x/NT format. Data is stored in .REG files using the following syntax:[21]

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In Windows, use of the registry for storing program data is a matter of developer's discretion. Microsoft provides programming interfaces for storing data in XML files (via MSXML) or database files (via SQL Server Compact) which developers can use instead. Developers are also free to use non-Microsoft alternatives or develop their own proprietary data stores.

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