Previously unreleased fission-track results and regional structural relationships are used to interpret the migration of deformation during Cenozoic orogenesis in the Eastern Cordillera (Cordillera Oriental) of the Colombian Andes. Low-temperature thermochronological results are based on apatite and zircon fission-track analyses of 41 samples collected along vertical and horizontal transects across the Eastern Cordillera at 4–7°N latitude. Inverse modeling of fission-track results helps delimit the most probable cooling histories caused by exhumation linked to upper-crustal deformation. These inverse models are constrained by known structural geometries, chronostratigraphy, biostratigraphy, and vitrinite reflectance data. Fission-track data and modeling results indicate a close correspondence in the timing and style of deformation along the western and eastern flanks of the Eastern Cordillera. East-directed fold-thrust deformation along the eastern boundary with the Llanos foreland basin was underway by the late Oligocene and early Miocene. Similarly, west-directed fold-thrust structures along the western boundary with the intermontane middle Magdalena Valley Basin became active at approximately the same time. Less well known is the time of initial shortening within the axial segment of the Eastern Cordillera; although fission-track results suggest active exhumation by the early Miocene, shortening may have commenced much earlier during the late Eocene. Timing relationships for the Eastern Cordillera have important implications for the generation, migration, and accumulation of petroleum in the middle Magdalena Valley intermontane basin and the Llanos foreland basin. Our study provides a regional context to assess the timing of structural trap development and improve exploration and development of new and existing reservoirs in Colombia and analogous fold-thrust systems elsewhere. Andrés Mora is a senior researcher and leader of the Cronologia de la deformaciòn en las Cuencas Subandinas research project at Ecopetrol-Instituto Colombiano del Petróleo. He received his B.Sc. degree in geology from the Universidad Nacional de Colombia in 1999 and his Ph.D. from the Institut für Geowissenschaften, Universität Potsdam (summa cum laude) in 2007. His research interests include structural geology, thermochronology, and basin analysis. Brian Horton is an associate professor at the Department of Geological Sciences and Institute for Geophysics in the Jackson School of Geosciences at the University of Texas at Austin. He received his B.S. degree in geology from the University of New Mexico (1992), his M.S. degree in earth sciences from Montana State University (1994), and his Ph.D. in geosciences from the University of Arizona (1998). His research interests include basin analysis, tectonics, and clastic sedimentology. Andrés Mesa is an exploration geologist who worked in Hocol S.A. from 2005 to 2009 and was in charge of an exploration and production contract in the Eastern Cordillera Basin. He received his B.Sc. degree in geology from the National University at Bogotá (Colombia) in 2005 and is currently doing an M.Sc. degree at Royal Holloway-University of London. His principal interest is basin analysis. Jorge Rubiano is a senior geologist at Ecopetrol-Instituto Colombiano del Petróleo. He obtained a B.Sc. degree from the National University at Bogotá (Colombia) and an M.Sc. degree in basin analysis from the University of South Carolina. Over the past years, he has worked for Ecopetrol on research projects addressing the stratigraphy, structure, basin evolution, and hydrocarbon systems of sedimentary basins in the northern Andes. Richard Ketcham is an associate professor of geological sciences at the University of Texas at Austin. He received his B.A. degree in geology and computer science from Williams College in 1987 and his Ph.D. in geological sciences from the University of Texas at Austin in 1995. His active research interests include thermochronology and geological applications of high-resolution x-ray computed tomography. Mauricio Parra graduated in geology from the National University of Colombia at Bogota in 2000 and received a Ph.D. in geosciences from Potsdam University (Germany) in 2009. He has worked in the tectonic evolution of the Colombian Andes and the associated foreland basin system using low-temperature thermochronometry and basin analysis. He is now a postdoctoral researcher at the Jackson School of Geosciences, University of Texas at Austin. Vladimir Blanco is the current leader of the organic geochemistry lab at Ecopetrol-Instituto Colombiano del Petróleo. He received his B.Sc. degree in geology from the Universidad Industrial de Santander at Bucaramanga (Colombia). He has worked on multiple projects from Ecopetrol since 2006 by giving technical support in basin modeling and characterization of source rocks and crude oils. Diego Garcia joined Ecopetrol-Instituto Colombiano del Petróleo (ICP) in 1998. He holds a diploma in geology from the National University at Bogotá (Colombia), an M.Sc. degree from the Institut Français du Pétrole School (France) on basin analysis, and a Ph.D. from the Federal University of Rio de Janeiro on petroleum and gas exploration. Currently, he is the technical leader of the geological research program of ICP. His research interests include the prediction of petroleum composition, thermal modeling, and the geological controls on petroleum migrations. Daniel Stockli is an associate professor in tectonics and thermochronometry at the University of Kansas and has been the director of the KU (U-Th)/He thermochronometry laboratory since 2001. He received his diploma in geology from the Eidgenössische Technische Hochschule Zürich in 1995 and his Ph.D. from Stanford University in 1999. His interests include continental tectonics, geo- and thermochronology, structural geology, and isotope geochemistry.