A multi-input single-output (MISO) semi-active control systems were studied by many researchers. For more improved vibration control performance, a structure requires more than one control device. In this paper, multi-input multi-output (MIMO) semi-active fuzzy controller has been proposed for vibration control of seismically excited small-scale buildings. The MIMO fuzzy controller was optimized by multi-objective genetic algorithm. For numerical simulation, five-story example building structure is used and two MR dampers are employed. For comparison purpose, a clipped-optimal control strategy based on acceleration feedback is employed for controlling MR dampers to reduce structural responses due to seismic loads. Numerical simulation results show that the MIMO fuzzy control algorithm can provide superior control performance to the clipped-optimal control algorithm.