Abstract Petroleum systems commonly develop in large sedimentary wedges. In Colombia, large sedimentary wedges exist along the Pacific active margin, along the Caribbean right-lateral transcurrent margin, and in the Middle Magdalena Valley basin. The Middle Magdalena basin Neogene sedimentary wedge gently laps onto the Precambrian/Lower Paleozoic metamorphic rocks of the west wall of the Middle Magdalena Valley basin, which is the Central Cordillera. The Central Cordillera is the northern extension of the Andean magmatic arc created by subduction of the Farallon/Cocos plates. This volcanic arc has been active, certainly during historic and present times. The end of Mesozoic-initiated subduction parallel to the Upper and Middle Magdalena Valley basins triggers the uplift of the Central and Eastern Cordilleras. The Eastern Cordillera, east of the Middle Magdalena Valley, displays abundant reflection seismic evidence of east to west thrusting involving Tertiary and Cretaceous valley sediments during Late Paleocene-Early Eocene, related to Central Cordillera uplift. Thrusting continues today to the west of the Eastern Cordillera, at a rate of several cm/ year. Low-grade deformation associated with thrusting can nucleate folds and lead to fracturing having no lateral movement. Such deformation can create non-steady state complex fluid flow at various scales, by opening and closing migration routes through fracture networks. Higher-grade compressional deformation, such as shortening across the Middle Magdalena Valley associated with the Eastern Cordillera uplift, inverts former extensional features during the Paleocene and middle to late Miocene. This structural inversion is documented in oil fields within the basin such as La Cira-Infantas giant oil field. Uneven advance of the thrust and deformation front in a vertical and lateral sense adds greater complexity to regional shortening of the Middle Magdalena Valley basin. The advance of the eastern wall (Eastern Cordillera) of the Middle Magdalena Valley basin is not continuous. Portions of the eastern wall advance more rapidly than others as evidenced by the uneven and irregular spacing of Holocene faults. Irregular deformation rates seen on the surface may also apply to the subsurface. From a petroleum system perspective, a sedimentary body less deformed than its neighbors may retain its fluid longer. When local deformation finally occurs, it may be relatively rapid. Fluid expulsion then can be more energetic than in adjacent areas, and a second phase of hydrocarbon migration takes place.