The authors analyze the complex problems associated with the formation of regional industrial clusters of really innovative type, with the introduction into the activities of the real economy scheme of public-private partnership, with the revival of the national pharmaceutical industry, in particular pharmaceutical industry and medical equipment industry. Solution of these problems, according to the authors, provide a procedure for import of foreign drugs quality Russian pharmaceuticals, which is currently the most important problems facing the society and the state. Degradable materials demonstrate the relevance of the issues raised in the article. The authors consider the pharmaceutical cluster of St. Petersburg, activities, participants, members of these relatively new form of territorial units, analyze the innovative activity of a number of existing companies a bearing producing both generic and original commercial products with innovative features. To identify the innovative leaders in the urban cluster applied technique of multidimensional comparative analysis in relation to the activities of the five relatively successful participants of the St. Petersburg pharmaceutical cluster. Were selected for analysis the important technical and economic indicators of commercial activity, one way or another reflect the industrial innovation. Draw the necessary conclusions, are specific proposals on the applicability of the recommended method of comparative analysis. It is shown that when overcoming any serious economic problem of modernization irrespective of its scale at the level of separately taken region the operational decision on places of questions of social and economic development and creation of necessary innovative potential is of particular importance. Thus the role of the state consists in creation and initial financing of necessary infrastructure for innovative activity of all types and forms and it is desirable according to efficient schemes of PPP/ChGP. Authors consider that further researches of the considered problems have to be connected with creation of the independent system of statistics estimating exactly and only innovative activity of economic subjects of pharmaceutical industry and also with development of the reasonable criteria of production localization of LS/LP released by domestic pharmaceutical clusters.