The results obtained using the method of structural epidemiological analysis in combination with the methods of selective statistics, comparative analysis of population morbidity, and development of personified medical databases for solving ecological problems are presented. It is shown that the interdisciplinary principle of organization of ecological studies implies the search for solution of the problem on discrepancy between the scientific and methodical level of ecological epidemiology and the level of development of the corresponding applied fields of mathematics, chemistry, and physics. The comparison of the results of ecological studies carried out in Novosibirsk within the framework of the currently accepted methods and those obtained with the use of the above-mentioned combination of methods showed that in the latter case the results are far more informative.