"Run As Administrator"

I don't know about Malwarebytes, don't use it, but usually running as administrator gives you full access to all functions of the program. If you run as a user then it usually limits what you can do.

In windows, up thru XP the main account was the administrator account and had full administrator privileges. That could be a bad situation if you hit some kind of nasty malware while in a full privilege account. Starting with Vista and continuing into Windows 7, microsoft put in "UAC" (User Account Control) which limits software to regular user privileges until you authorize it to use administrator privileges. "Run As Administrator" is one of the ways to authorize it.

Just like Sci-Fi says.

You generally DON'T want to run programs as an administrator, as it can be dangerous and leave your system open to infection. Running as admin opens control systems that a casual, generic user wouldn't necessarily need, and if mismanaged, will only cause harm to your computer.

The UAC is there for security purposes. The idea being so that you would not be running everything with admin privileges. The reasoning is as BJD says.

Some programs do run with full admin privileges though it may not be noticeable unless they set off the UAC prompt. Since the question is specifically about Malwarebytes, i will paste in their explanation of why the free version sets off the UAC prompt.

"mbam.exe requires administrative privileges to run for several reasons, the first is scanning: in order to check all locations that it wants to, it must have administrative access, the second is removal: in order to delete a file or registry entry that is in a privileged location, it requires administrative access, the third is the database: our database file (rules.ref) is stored in a central location for all users, so that if one user updates, all other user accounts on the system update along with it without having to perform updates from each profile, and administrative privileges are required to write to that location.

Other security software (AV's etc.) will use a service to execute all of these tasks, and the service has sufficient privileges to grant administrative access to their program for updating, scanning and removal. Ours could technically do so, but since our PRO version and Free version are the same program, just with different features and our Free version does not install a service that runs whenever you boot your PC to handle such tasks, it must universally require administrative privileges for mbam.exe to perform such tasks."

Basically means your "Big Daddy"