Fugitive losses from natural gas distribution systems are a significant source of anthropogenic methane. Here, we report on a national sampling program to measure methane emissions from 13 urban distribution systems across the U.S. Emission factors were derived from direct measurements at 230 underground pipeline leaks and 229 metering and regulating facilities using stratified random sampling. When these new emission factors are combined with estimates for customer meters, maintenance, and upsets, and current pipeline miles and numbers of facilities, the total estimate is 393 Gg/yr with a 95% upper confidence limit of 854 Gg/yr (0.10% to 0.22% of the methane delivered nationwide). This fraction includes emissions from city gates to the customer meter, but does not include other urban sources or those downstream of customer meters. The upper confidence limit accounts for the skewed distribution of measurements, where a few large emitters accounted for most of the emissions. This emission estimate is 36% to 70% less than the 2011 EPA inventory, (based largely on 1990s emission data), and reflects significant upgrades at metering and regulating stations, improvements in leak detection and maintenance activities, as well as potential effects from differences in methodologies between the two studies.