Cities dominate greenhouse gas emissions. Many have generated self-reported emission inventories, but their value to emissions mitigation depends on their accuracy, which remains untested. Here, we compare self-reported inventories from 48 US cities to independent estimates from the Vulcan carbon dioxide emissions data product, which is consistent with atmospheric measurements. We found that cities under-report their own greenhouse gas emissions, on average, by 18.3% (range: -145.5% to +63.5%) - a difference which if extrapolated to all U.S. cities, exceeds California's total emissions by 23.5%. Differences arise because city inventories omit particular fuels and source types and estimate transportation emissions differently. These results raise concerns about self-reported inventories in planning or assessing emissions, and warrant consideration of the new urban greenhouse gas information system recently developed by the scientific community.