Beware of paying subordination fees in a mortgage refinance. Refinance your mortgage twice and you might be paying subordination fees during the mortgage refinance. If you refinance your home mortgage with two lenders, you may be responsible for paying subordination fees. Paying subordination fees in mortgage refinance marks one lender as the primary mortgage lender and one as the secondary mortgage lender. Paying subordination fees in mortgage refinance allows the primary mortgage lender to grant your mortgage refinance. Make sure you understand paying subordination fees in mortgage refinance when refinancing your home mortgage a second time.