An exceptional analogue for the study of the causes and consequences of global warming occurs at the Palaeocene/Eocene Thermal Maximum, 55 million years ago. A rapid rise of global temperatures during this event accompanied turnovers in both marine and terrestrial biota, as well as significant changes in ocean chemistry and circulation. Here we present evidence for an abrupt shift in deep-ocean circulation using carbon isotope records from fourteen sites. These records indicate that deep-ocean circulation patterns changed from Southern Hemisphere overturning to Northern Hemisphere overturning at the start of the Palaeocene/Eocene Thermal Maximum. This shift in the location of deep-water formation persisted for at least 40,000 years, but eventually recovered to original circulation patterns. These results corroborate climate model inferences that a shift in deep-ocean circulation would deliver relatively warmer waters to the deep sea, thus producing further warming. Greenhouse conditions can thus initiate abrupt deep-ocean circulation changes in less than a few thousand years, but may have lasting effects; in this case taking 100,000 years to revert to background conditions.