Natural gas is the largest source of anthropogenic emissions of methane (CH4) in the United States. To assess pipeline emissions across a major city, we mapped CH4 leaks across all 785 road miles in the city of Boston using a cavity-ring-down mobile CH4 analyzer. We identified 3356 CH4 leaks with concentrations exceeding up to 15 times the global background level. Separately, we measured δ13CH4 isotopic signatures from a subset of these leaks. The δ13CH4 signatures (mean = -42.8‰ ± 1.3‰ s.e.; n = 32) strongly indicate a fossil fuel source rather than a biogenic source for most of the leaks; natural gas sampled across the city had average δ13CH4 values of -36.8‰ (±0.7‰ s.e., n = 10), whereas CH4 collected from landfill sites, wetlands, and sewer systems had δ13CH4 signatures ~20‰ lighter (μ = -57.8‰, ±1.6‰ s.e., n = 8). Repairing leaky natural gas distribution systems will reduce greenhouse gas emissions, increase consumer health and safety, and save money.