In this paper, the probabilistic seismic performance of vertically irregular steel buildings, considering soil-structure interaction effects, is evaluated. Various irregular distributions of structural properties, including mass, stiffness and strength along the height of three-dimensional moment resisting steel frames were intended. The finite element model of soil medium was created with solid elements below the structure. The nonlinear material behavior of soil was considered as well. Nonlinear incremental dynamic analysis was performed to evaluate the flexible-base structural performance in the framework of probabilistic performance-based earthquake engineering. According to the median curves of intensity-demand of structures, it is concluded that non-uniform height-wise distribution of lateral resistance properties of steel structures varies the displacement demand and the seismic capacity of the irregular frames, compare to the regular structure. The capacity variation of most irregular frames is more obvious at the nonlinear phase of structural behavior. Due to the foundation flexibility, the damage concentration raises in the bottom floor and the irregularity increase the seismic demands of the lower floors of the system. Among all the irregular steel frames, the average increase of the displacement demand and reduction of the seismic capacity are maximal for the strength and concurrent variation of stiffness and strength irregularity models, respectively. Additionally, mass irregularity shows minor influence in the seismic demand and capacity variations of the steel frames. The predominant influence of stiffness and strength irregularities (soft and weak story) is observed in reduction of the structural ductility factor and the mean annual frequency of exceeding limit states.