Prior to IIS 6.0 all the webapplications used to run at the same place in iis server.
When one webapplication get affected that in turn used to effect all the webapplications running in the server.
So in IIS 6.0 a new concept called Application Pool came in to picture.
Application pools provide a isolation between the webapplications so that when one worker process or application is having an issue or recycles, other applications or worker processes are not affected.
So in this way Apllication pools provide more security and reliability with the concept of isolation.
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