The time-varying deformation field within a fault zone, particularly at depths where earthquakes occur, is important for understanding fault behaviour and its relation to earthquake occurrence. But detection of this temporal variation has been extremely difficult, although laboratory studies have long suggested that certain structural changes, such as the properties of crustal fractures, should be seismically detectable. Here we present evidence that such structural changes are indeed observable. In particular, we find a systematic temporal variation in the seismograms of repeat microearthquakes that occurred on the Parkfield segment of the San Andreas fault over the decade 1987-97. Our analysis reveals a change of the order of 10 m in the location of scatterers which plausibly lie within the fault zone at a depth of approximately 3 km. The motion of the scatterers is coincident, in space and time, with the onset of a well documented aseismic transient (deformation event). We speculate that this structural change is the result of a stress-induced redistribution of fluids in fluid-filled fractures caused by the transient event.