The changes will see reductions to the basic filing fee for utility patents (down to $280 from $380 for large entities) and design patents (reduced from $250 to $180).
Issue fees will be reduced and the $300 publication fee will be abolished in January 2014.
But maintenance fees are being increased, by between 26% and 56%.
There are also changes to claim fees, RCE fees, appeals, ex parte re-examination and inter partes reviews.
The fee changes result from the America Invents Act, which requires the USPTO to recover sufficient fees to cover its costs.
The agency proposed fee rules in September last year, and has reduced some fees in response to feedback received since then.
There are discounts for small and micro entities of up to 75% on many fees.
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