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What is the difference between an on-board VGA port and a VGA port provided by the video card? Is it possible to have an extended display using one VGA port from on-board and one from the video card?

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Not much at all - its just the output for some video device. However, many motherboards, especially older ones use the same PCI-E lane for both integrated and external graphics - if so you won't be able to use both at once - see this answer for details on that.

Newer systems, especially those with on-package video processors, such as the intel sandy and ivy bridge as well as AMD APU based systems shouldn't have this issue since they don't use the external PCI-E bus to for communications between the IGP and the rest of the system.

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Just keep in mind that using monitors on fundamentally different video hardware at the same time is only officially supported on Windows 7. If you have Vista or XP, it won't work except with a small number of hardware combinations. –  David Schwartz Jun 26 '12 at 6:32

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