Jakobshavn Isbræ is the most active glacier in Greenland, with an annual discharge of about 30 km3 of ice, and it is one of the few recently surveyed glaciers to thicken between 1993 and 1998, despite locally warm summers. Repeated airborne laser-altimeter surveys along a 120 km profile in the glacier basin show slow, sporadic thickening between 1991 and 1997, suggesting a small positive mass balance, but since 1997 there has been sustained thinning of several m a−1 within 20 km of the ice front, with lower rates of thinning further inland. Here, we use weather-station data from the coast and the ice sheet to estimate the effects on surface elevation of interannual variability in snowfall and surface melt rates, and thus to infer the temporal and spatial patterns of dynamic thinning. These show the glacier to have been close to balance before 1997 followed by a sudden transition to rapid thinning, initially confined to the lower reaches of the glacier (below about 500 m elevation), but progressively spreading inland until, between 1999 and 2001, thinning predominated over the entire surveyed region, up to 2000 m elevation. If this continues, the glacier calving front and probably its grounding line will retreat substantially in the very near future.