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There is a site that seems to work only when I visit it without a VPN. Sometimes I like to use a VPN but then I can never get the webpage to work. What I want to know is whether there is any way a website can figure out if one is using a VPN while accessing it?

Win 7. IE 9.

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Your IP Address will be different when using via VPN. It would be of the VPN Provider. Maybe the site has blocked access from that VPN Provider, try with someother VPN (they might have trial offers.)

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But can a site know if you are using a VPN? – verve Jun 12 '12 at 7:39
Nope. @grawity below has given a good answer. – KGA Jun 14 '12 at 3:26

From the web server's point of view, both are identical TCP/IP connections, just coming from different locations. The server cannot see which route the packets traveled, and doesn't automagically know that there's a VPN server running at a certain address.

However, a server can be configured to, for example, only allow (or deny) connections from certain addresses. If the VPN is a public service, then its IP address blocks are often listed somewhere, and might be blocked by some administrators (depending on the service's popularity and/or abuse record). The opposite is also possible – some VPN services explicitly deny access to certain web sites.

Finally, since the VPN server is at a different location than you are, it is possible that there are network problems somewhere between web and VPN servers, that just have gone unnoticed because nobody complained.

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