Principles of data analysis, which were got during developing inventory of multifactor research of tolerance, are observed. This inventory has two-mode structure. The necessity of studying of tolerance as complex system including possible objects of tolerant attitude along with different possible levels of regulations these attitudes was advocated. The structural equation modeling namely multi-trait multi-method model (MTMM) was used. Equations for specification the models are included. The possibility and advantages of using MTMM for analysis data having 3-mode structure in studies of different types is discussed.