Observations of distant supernovae and the fluctuations in the cosmic microwave background (CMB) indicate that the expansion of the Universe may be accelerating under the action of a `cosmological constant' or some other form of `dark energy'. This dark energy now appears to dominate the Universe and not only alters its expansion rate, but also affects the evolution of fluctuations in the density of matter, slowing down the gravitational collapse of material (into, for example, clusters of galaxies) in recent times. Additional fluctuations in the temperature of CMB photons are induced as they pass through large-scale structures and these fluctuations are necessarily correlated with the distribution of relatively nearby matter. Here we report the detection of correlations between recent CMB data and two probes of large-scale structure: the X-ray background and the distribution of radio galaxies. These correlations are consistent with those predicted by dark energy, indicating that we are seeing the imprint of dark energy on the growth of structure in the Universe.