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The USPTO receives its operating funds through application fees, officially designated as "offsetting collections" to be placed in the Patent and Trademark Office Appropriations Account. However, the office must publish annal reports to Congress on its expected level of revenue and expenditure. From there, Congress appropriates a certain level of funding that the USPTO may keep form its fee collection in order to run the office. Essentially, the USPTO must request permission to keep and use the money it receives from the application fees. No additional appropriation through Congress is usually approved. The net appropriation for the past three years has been $0.
 
The Leahy-Smith America Invents Act (AIA) created a reserve fund for the USPTO, where all excess fees are to be deposited. Further, the AIA granted the USPTO authority "to set or adjust by rule any fee established or charged by the Office". This provision increased the office's flexibility on fee setting and helped pave the way for a new class of fees for "micro entities."[http://www.uspto.gov/custom-page/inventors-eye-advice]
For FY 2016, the office requested $3.2 billion of allowed expenditure from its fee collections, which with funds from other income and the Operating reserve balance, is expected to fund the necessary operating budget of $3.5 billion.[http://www.uspto.gov/sites/default/files/documents/fy16pbr.pdf]
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