The toilet rough-in refers to the distance from the finished wall to the center of the toilet's floor drain or waste outlet.
Most toilets have a rough-in of 12 inches, although it's not uncommon for older homes to have an unusual size such as 10" or 14". Take the time to measure, never assume, and be sure that the toilet you decide to purchase is compatible.
When measuring, you should measure from the finished wall - not from the baseboard or molding. A well-measured rough in will keep you from having to make unnecessary adjustments or returning a toilet. If you aren't able to see the center of the drain (i.e. you already have a toilet in place), measure from the wall to the center of the bolt caps. There are usually two bolt caps, one on either side of the toilet.
Rear-outlet toilets are configured a bit differently. Rather than waste exiting through the floor, it exits through the bathroom wall. The rough-in measurement for a rear-outlet toilet is the distance from the finished floor to the center of the waste outlet.
For more useful information about selecting the right toilet for your home, check out our Toilet Buying Guide.