We estimate strong ground motions in Kobe during the Hyogo-ken Nanbu earthquake of 1995 by using a three-dimensional (3-D) basin structure. A 3-D finite difference method with fourth ordered staggered-grid scheme developed by Graves (1996) is used. We first calculate bedrock motions generated by the inverted source model of Wald (1996) to see how well it can reproduce the observed bedrock motions. A realistic 3-D basin model is then constructed based on the exploration data and is used to calculate synthetic motions. We found that Wald's source model reproduces observed waveforms only in the long-period range, where the basin-edge effect does not contribute much. To make the input motion more realistic we convolve the synthetic bedrock motion with the bedrock motion inverted from the observed record at JMA. The resultant synthetic waveforms on the surface of the 3-D basin are very similar to the observed and the contribution of the edge effect becomes almost the same order as that of the direct S-wave. It means that both the deep 3-D basin structure and the detailed rupture process of the fault have to be taken into account to simulate the strong ground motions quantitatively.