The recent growth in production and utilization of natural gas offers potential climate benefits, but those benefits depend on lifecycle emissions of methane, the primary component of natural gas and a potent greenhouse gas. This study estimates methane emissions from the transmission and storage (T&S) sector of the United States natural gas industry using new data collected during 2012, including 2,292 onsite measurements, additional emissions data from 677 facilities and activity data from 922 facilities. The largest emission sources were fugitive emissions from certain compressor-related equipment and "super-emitter" facilities. We estimate total methane emissions from the T&S sector at 1,503 [1,220 to 1,950] Gg/yr (95% confidence interval) compared to the 2012 Environmental Protection Agency's Greenhouse Gas Inventory (GHGI) estimate of 2,071 [1,680 to 2,690] Gg/yr. While the overlap in confidence intervals indicates that the difference is not statistically significant, this is the result of several significant, but offsetting, factors. Factors which reduce the study estimate include a lower estimated facility count, a shift away from engines toward lower-emitting turbine and electric compressor drivers, and reductions in the usage of gas-driven pneumatic devices. Factors that increase the study estimate relative to the GHGI include updated emission rates in certain emission categories and explicit treatment of skewed emissions at both component and facility levels. For T&S stations that are required to report to the EPA's Greenhouse Gas Reporting Program (GHGRP), this study estimates total emissions to be 260% [215% to 330%] of the reportable emissions for these stations, primarily due to the inclusion of emission sources that are not reported under the GHGRP rules, updated emission factors, and super-emitter emissions.