Collisions between small bodies (such as asteroids and comets) and the terrestrial planets are known to throw ejecta far beyond the point of impact. But until the fragments of comet Shoemaker-Levy 9 hit Jupiter in July 1994 (refs 1, 2), there had been no opportunity to study the effects of such collisions on gas-giant planets. Here we present optical spectra obtained during the collision of fragments L and Q(1), with Jupiter. We observed emission lines from sodium, magnesium, calcium, iron, manganese and chromium as the ejecta plume fell back onto Jupiter’s atmosphere. All of these elements are expected to occur only very deep in Jupiter’s atmosphere-considerably below the depth to which the fragments penetrated--, suggesting that the material responsible for the emissions originated almost entirely in the comet itself. The initial. phase of emission is associated with heating of the impact ejecta as it fell back onto the planet. A second, later phase of emission was also observed, which we associate with grains of silicate dust that condensed within the cooling fireball and subsequently re-entered, meteor-like, into Jupiter’s atmosphere.