I have what looks like red spots inside my double pane windows , what can it be?

Can I assume you mean thermopane windows?

Yes , they are 12 years old

A failed therompane allows the gases out and air and moisture in between the panes. I have never seen this but there is no reason why mold can't start growing. There are a few companies that claim they can repair faired therompanes but your original window may still be under warranty. Do you know the brand and did you have them put in?

No but they are original and we just bought the place

Time to start surfing sites like “Get the Fog Out” of Thermopane Windows at Home Ray Sands Glass Blog (http://raysands.wordpress.com/2008/09/10/get-the-fog-out-of-thermopane-windows-at-home/) or try to find out the brand