I'm sure an expert will chime in, but I'm pretty sure the "note rate" is the raw annual percent interest for the loan, and the APR takes into account fees and compounding to express your total annual cost for the loan. To show the effect of compounding, consider the interest that WaMu is currently offering for their on-line savings. They say the rate is 3.93%, and the APR is 4%. The interest is compounded monthly, so each month you earn 3.93%/12=0.3275% interest on your balance. Over the course of the year, you effectively get (100.3275%)^12 = 104%.