We estimated the amount of carbon (C) stored in terrestrial ecosystems of the Chilean Patagonia and the proportion within protected areas. We used existing public databases that provide information on C stocks in biomass and soils. Data were analysed by ecosystem and forest type in the case of native forests. Our results show that some ecosystems have been more extensively studied both for their stocks in biomass and soils (e.g. forests) compared with others (e.g. shrublands). Forests and peatlands store the largest amount of C because of their large stocks per hectare and the large area they cover. The total amount of C stored per unit area varies from 261.7 to 432.8 Mg C ha(-1), depending on the published value used for soil organic C stocks in peatlands, highlighting the need to have more precise estimates of the C stored in this and other ecosystems. The mean stock in national parks (508 Mg C ha(-1)) is almost twice the amount stored in undisturbed forests in the Amazon. State and private protected areas contain 58.9% and 2.1% of the C stock, respectively, playing a key role in protecting ecosystems in this once pristine area.