Facility-level methane emissions measurements were conducted using a new dual tracer gas technique at 130 natural gas gathering facilities and processing plants in 13 U.S. states. The results from the field campaign were combined with state and national facility databases in a Monte Carlo simulation to estimate methane emissions from U.S. natural gas gathering and processing operations. Total annual methane emissions of 2,421 (+245/-237) Gg were estimated for all U.S. gathering and processing operations, representing a methane loss rate of 0.47% (±0.05%) when normalized by 2012 CH4 production. The largest source of methane emissions from gathering and processing operations were attributed to normal operation of gathering facilities (1,697 +189/-185 Gg) and these emissions were eight times that of previous EPA Greenhouse Gas Inventory (GHGI) estimates. The methane emissions from processing plants (506 +55/-52 Gg) were 40% lower than previous GHGI estimates but a factor of three higher than that reported under the EPA Greenhouse Gas Reporting Program (GHGRP). In April 2016, the EPA GHGI was updated based directly on the results of this study, which effectively added over 1500 Gg of annual methane emissions to the inventory. With these updates to the EPA GHGI, gathering operations are now estimated to account for 27% of all methane emissions from natural gas supply chain.