Studies of the geodynamic evolution of Southeast Asia have resulted in a number of tectonic reconstructions that exhibit a broad consensus as well as significant differences. In this contribution we apply a method to further test these surface reconstructions, using independent seismic tomography results. Our kinematic modelling procedure comprises the calculation of three-dimensional forward models of the seismic velocity structure beneath Indonesia. From information contained in the tectonic reconstructions, the effect of the proposed surface motions on the thermal structure of the underlying mantle is modelled. This results in a prediction of the present-day temperatures which are converted into seismic (P-wave) velocity anomalies. By comparing the predicted velocity models with recent tomography results of the area, the quality of the tectonic reconstructions can be evaluated. The models presented in this paper are based on the reconstructions of Rangin et al. (Bull. Soc. Géol. France, 8 (1990a) 889; Bull. Soc. Géol. France, 8 (1990b) 907) and Lee and Lawver (Tectonophysics, 251 (1995) 85). In general, we conclude that the calculated positive velocity anomalies beneath the Sunda and Banda arc show strong similarities with the tomography results. The modelled patterns of high velocities beneath southern Sulawesi are not found in the tomographic images. The model predicted from Rangin et al. (1990a,b) does not show the double-sided subduction under the Molucca Sea region that can be seen in the model predicted from Lee and Lawver (1995) and in the tomographic model. Our results indicate the potential of the method for investigating the geodynamic evolution of the Indonesian region.