The polar ice sheets, their surrounding land fringes and oceans (68 × 106 km2; 13% of Earth's surface) are hot spots for carbon cycle perturbation under future climate change due to glacier retreat, rising meltwater fluxes, reduced sea ice, thawing permafrost, warming land-surfaces and increased precipitation. Here we assess carbon stored and exchanged with the atmosphere (as carbon dioxide and methane) across an expansive bipolar ice-to-ocean domain. We show that the polar regions harbor large reserves of carbon stored in sediments, rocks and the ocean, which differ in their reactivity and turnover times: 5,300–22,200 PgC of organic carbon and 5,600–8,600 PgC of inorganic carbon. These carbon reservoirs include potential reserves of marine and subglacial methane hydrate (80–570 PgC), which could become destabilized under future warming scenarios. Oceans (270–360 PgC) and ice sheets (14–96 PgC Greenland, 5,000–21,000 PgC Antarctica) dominate organic carbon stores, with smaller (but regionally important) stocks found in ice sheet land fringes (13–58 PgC). Estimates of natural CO2 and CH4 fluxes from these polar regions to the atmosphere present high uncertainty but highlight oceanic CO2 sinks in Greenland (−110 to −49 TgC-CO2 a−1) and in the ICE and SPSS biomes of the Southern Ocean (−480 to 55 TgC-CO2 a−1), with potential CH4 sources associated with the Greenland Ice Sheet. Such high uncertainty in polar carbon reservoirs and fluxes is important to resolve if future feedbacks between the polar regions, Earth's carbon cycle and climate are to be conclusively determined.