Why APR Alone Is a Poor Way to Compare Mortgages "Just choose the lowest APR." If only mortgage shopping were that simple. APR includes the interest rate and certain financing charges. But it does not know your plans to sell, refinance, or make extra principal payments. You may be planning a three-year relationship with the mortgage. APR is doing the math for a 30-year marriage. Lender credits can also muddy the comparison. One lender charges you $600 for an appraisal. Anothe