If a mortgage company gives you a Good Faith Estimate of your closing costs, they are required by Federal Law to give you a Federal Truth In Lending form.  The APR is on this form.  The APR is intended to be your "shopping tool".  The lower the "spread" between your actual interest rate and your APR, the less you paid to get your loan.

Example:
Loan one has an interest rate of 5% with an APR of 5.5%.
Loan two has an interest rate of 5% with an APR of 5.25%.

Loan one has an APR that is .25% higher than loan two, because the fees to do loan one are much, much higher than they are on loan two!

Did you get a Truth In Lending when you got your Good Faith Estimate?  If not, they may be trying to hide something.  Be careful when you hear about a low, low interest rate - the fees could be astronomical!