The USDA program has changed. Effective October 1, 2012 it will no longer be subsidized by the US Taxpayer. Effective October 1, 2012, USDA mortgage insurance rates are: For purchases, 2.00% upfront fee paid at closing, based on the loan size.For refinances, 2.00% upfront fee paid at closing, based on the loan size.For all loans, 0.40% annual fee, based on the remaining principal balance. A $100,000 loan would require a $2,000 mortgage insurance payment at closing, and $33.33 of mortgage insurance (1 comments)