July 1994, the collisions of the fragments of comet Shoemaker-Levy 9 with Jupiter resulted in dramatic changes in the planet’s atmosphere. Observations of the events suggest that the composition and thermal properties of the atmosphere were considerably modified at the impact sites, with the changes persisting for times lasting from minutes to weeks (see, for example, refs 1-4). Here we report observations of the impact sites at millimetre wavelengths, which reveal strong emission lines associated with carbon monoxide, carbonyl sulphide and carbon monosulphide. The abundance of carbon monoxide in the jovian atmosphere is normally very low(5); carbonyl sulphide and carbon monosulphide, on the other hand, have not hitherto been detected, We find that the largest fragments (G and K) each produced approximately 10(14) g of carbon monoxide, 3 x 10(12) g of carbonyl sulphide and 3 x 10(11) g of carbon monosulphide, most probably by shock-induced chemical reactions(6). Our observations also place firm constraints on the thermal response of Jupiter’s stratosphere to the impacts.