Seismic refraction profiles were carried out in 1983 and 1987 throughout the Kerguelen Isles (southern Indian Ocean, Terres Australes & Antarctiques Franqaises, TAAF) and thereafter at sea on the Kerguelen‐Heard Plateau during the MD66/KeOBS cruise in 1991. These profiles substantiate the existence of oceanic‐type crust beneath the Kerguelen‐Heard Plateau stretching from 46°s to 55°S, including the archipelago. Seismic velocities within both structures are in the range of those encountered in ‘standard’ oceanic crust. However, the Kerguelen Isles and the Kerguelen‐Heard Plateau differ strikingly in their velocity‐depth structure. Unlike the Kerguelen Isles, the thickening of the crust below the Kerguelen‐Heard Plateau is caused by a 17 km thick layer 3. Velocities of 7.4 km s−1 or so within the transition to mantle zone below the Kerguelen Isles are ascribed to the lower crust intruded and/or underplated by upper mantle material. The crust‐mantle boundary below the Kerguelen‐Heard Plateau is abrupt and devoid of any underplated material. The difference in structure between the northern edge of the Kerguelen Plateau (including the archipelago) and the Kerguelen‐Heard Plateau may be related to variability of the time‐dependent hotspot activity. The Kerguelen‐Heard Plateau was emplaced during the Cretaceous time (110 Ma) when the volcanic output rate of the Kerguelen Plateau and the Ninetyeast Ridge was high (as well as high potential temperature). The northernmost Kerguelen Plateau and the archipelago were emplaced during Tertiary time (40–45 Ma), as the volcanic output rate reduced. Furthermore, intraplate volcanism continued in the Kerguelen archipelago for at least 40 Ma. The isostatic compensation of the Kerguelen Isles and the Kerguelen‐Heard Plateau is achieved by low‐density mantle material, as shown by refraction and geoid studies. The velocity‐depth structure below the Kerguelen Isles is similar to that found below intraplate oceanic islands such as Hawaii. Despite the differences in age, the crust below Iceland (0Ma) and the Kerguelen Plateau (100–120 Ma) are strikingly akin. The similarity between the Kerguelen‐Heard Plateau and Iceland, then, strongly supports a similar origin for both structures, the Kerguelen‐Heard Plateau being a fossil equivalent of present‐day Iceland. Crustal thickening beneath the Kerguelen‐Heard Plateau, which may result from an Iceland‐type setting (i.e. an active spreading centre over a hotspot), is mostly produced by thickening of layer 3, layer 2 representing 25 per cent only of the thickness of the igneous crust. The Kerguelen Isles, despite the initial volcanism near the active Southeast Indian Ridge, behave as a midplate volcanic island and are definitely not representative of the whole Kerguelen Plateau structure.