New facility-level methane (CH4) emissions measurements obtained from 114 natural gas gathering facilities and 16 processing plants in 13 U.S. states were combined with facility counts obtained from state and national databases in a Monte Carlo simulation to estimate CH4 emissions from U.S. natural gas gathering and processing operations. Total annual CH4 emissions of 2421 (+245/-237) Gg were estimated for all U.S. gathering and processing operations, which represents a CH4 loss rate of 0.47% (±0.05%) when normalized by 2012 CH4 production. Over 90% of those emissions were attributed to normal operation of gathering facilities (1697 +189/-185 Gg) and processing plants (506 +55/-52 Gg), with the balance attributed to gathering pipelines and processing plant routine maintenance and upsets. The median CH4 emissions estimate for processing plants is a factor of 1.7 lower than the 2012 EPA Greenhouse Gas Inventory (GHGI) estimate, with the difference due largely to fewer reciprocating compressors, and a factor of 3.0 higher than that reported under the EPA Greenhouse Gas Reporting Program. Since gathering operations are currently embedded within the production segment of the EPA GHGI, direct comparison to our results is complicated. However, the study results suggest that CH4 emissions from gathering are substantially higher than the current EPA GHGI estimate and are equivalent to 30% of the total net CH4 emissions in the natural gas systems GHGI. Because CH4 emissions from most gathering facilities are not reported under the current rule and not all source categories are reported for processing plants, the total CH4 emissions from gathering and processing reported under the EPA GHGRP (180 Gg) represents only 14% of that tabulated in the EPA GHGI and 7% of that predicted from this study.