The authors analyze the complex problems associated with the formation of regional industrial clusters of the truly innovative type, with the introduction of the public-private partnership scheme into the activities of the real economy, with the revival of the national medical industry, and, in particular, the pharmaceutical industry. Solving these problems, according to the authors, would provide a procedure for substituting foreign drugs with quality Russian pharmaceutical production, which is currently one of the most important problems facing the society and the state. The information described demonstrates the relevance of the issues raised in the article. The authors consider the pharmaceutical cluster of St. Petersburg, the activities of the participants of these relatively newly-formed territorial units, analyze the innovative activity of a number of existing companies producing both generic and original commercial products with innovative features. To identify innovative leaders in the cluster, we used a multidimensional comparative analysis technique. The paper contains the conclusions reached and some proposals.