For small-size reinforce-concrete buildings, Midas Gen, OpenSees, and Perform-3D, which are structural analysis programs that are most popularly used at present, were applied for nonlinear static pushover analysis, and then difference between those programs was analyzed. Example buildings were limited to 2-story frames with irregular shaped walls. Analysis result showed that there were more differences than for frames only and frames with rectangular walls, but it was not so significant. Nevertheless, the capacity curve were different in some buildings, which is attributed to shape and location of walls, and feature of the analysis program. Especially, selection of automatic or manual input in Midas Gen, or nonlinear wall elements in Perform3D can affect the capacity curve and performance of the buildings. Therefore, the program users should understand the feature of the program well, and then conduct performance assessment. The result of this study is limited to low-story buildings so that it should be noted that it is possible to get different results for mid- to high-rise buildings.