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The effects of complex wall structures on the characteristics of fading and the capacity of multi-input multi-output (MIMO) wireless communication systems for some typical indoor propagation environments are investigated. Two cases of wall structures are examined in this paper. In the first case, the walls are considered to be homogenous solid slabs, while, in the second case, the walls are assumed to be of complex structures. A two-dimensional finite difference time domain method is employed to calculate the electric field distributions, and then, the local mean power, the Rician K factor, and the MIMO capacity are calculated and analyzed. It is found that the patterns of the local mean power distributions are different for the two wall-structure cases. As for the small-scale fading, it is shown that the Rician K factors for the two cases may be different by 5 dB. The resulting values of MIMO capacities are also quite different and are less than the ideal cases, where the elements of the transfer (H) matrix are assumed to be zero-mean Gaussians with unit variance. We also investigate the cases where complex walls are replaced by effective slab walls. It is found that complex walls cannot be appropriately characterized by simple effective slab walls as considerable difference exists between the two cases.