Tropical forests play an important role in the global carbon cycle, as they store a large amount of carbon (C). Tropical forest deforestation has been identified as a major source of CO2 emissions, though biomass loss due to fragmentation-the creation of additional forest edges-has been largely overlooked as an additional CO2 source. Here, through the combination of remote sensing and knowledge on ecological processes, we present long-term carbon loss estimates due to fragmentation of Neotropical forests: within 10 years the Brazilian Atlantic Forest has lost 69 (+/- 14) Tg C, and the Amazon 599 (+/- 120) Tg C due to fragmentation alone. For all tropical forests, we estimate emissions up to 0.2 Pg Cy-1 or 9 to 24% of the annual global C loss due to deforestation. In conclusion, tropical forest fragmentation increases carbon loss and should be accounted for when attempting to understand the role of vegetation in the global carbon balance.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundacao O Boticario de Protecao a NaturezaBMBF (German Federal Ministry of Education and Research)Brazilian Science Council (Conselho Nacional de Desenvolvimento Cientifico)ERC advanced grantBMBFDepartment of Ecological Modelling of the Helmholtz Centre for Environmental Research (UFZ)Helmholtz Association of German Research Centres within the project 'Biomass and Bioenergy systems'Helmholtz-Alliance Remote Sensing and Earth System DynamicsFORMIND projectUFZ Helmholtz Ctr Environm Res, Dept Ecol Modelling, D-04318 Leipzig, GermanyUFZ Helmholtz Ctr Environm Res, Dept Bioenergy, D-04318 Leipzig, GermanyUFZ Helmholtz Ctr Environm Res, Dept Conservat Biol, D-04318 Leipzig, GermanyUniv Auckland, Sch Environm, Auckland 1, New ZealandUniv Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, CanadaFdn Edmund Mach, Ist Agr San Michele All Adige, I-38010 San Michele All Adige, TN, ItalyUniv Sao Paulo, Inst Biociencias, Dept Ecol, BR-05508900 Sao Paulo, BrazilUniv Estadual Paulista Julio Mesquita Filho UNESP, Inst Biosci, Dept Ecol, Spatial Ecol & Conservat Lab LEEC, BR-13506900 Rio Claro, BrazilUniv Osnabruck, Inst Environm Syst Res, D-49076 Osnabruck, GermanyGerman Ctr Integrat Biodivers Res iDiv, D-04103 Leipzig, GermanyUniv Estadual Paulista Julio Mesquita Filho UNESP, Inst Biosci, Dept Ecol, Spatial Ecol & Conservat Lab LEEC, BR-13506900 Rio Claro, BrazilFAPESP: 99/05123-4FAPESP: 01/13309-2FAPESP: 02/02125-0FAPESP: 02/02126-7CNPq: 690144/01-6BMBF (German Federal Ministry of Education and Research)01LB0202Brazilian Science Council (Conselho Nacional de Desenvolvimento Cientifico)307934/2011-0Brazilian Science Council (Conselho Nacional de Desenvolvimento Cientifico)312045/2013-1ERC advanced grant233066BMBF01LB0202