The article deals with the development of regional pharmaceutical clusters. We study the development of the Russian pharmaceutical market. It has been highlighted areas where there are promising pharmaceutical companies engaged in innovative activities and using modern marketing strategies, including breakthrough positioning strategy. The aim is to develop a tool positioning regional pharmaceutical cluster region-specific manufacturers and features segments of the pharmaceutical market, including: formulations, dietary supplements and biotechnology (cell and gene) products. Objectives of the work associated with the identification of the structure of the pharmaceutical market, the definition of its specificity, identifying the specific application and development of breakthrough strategies with them through regional pharmaceutical clusters. In this paper we use the matrix method and the method of a breakthrough positioning innovative products analyzed regional pharmaceutical cluster the directions of the strategy and development of a cluster of St. Petersburg. The results of the work related to the definition of the structure and features of the pharmaceutical market segments. Obtained promising areas of pharmaceutical cluster of St. Petersburg. The paper concludes that in the present conditions, the pharmaceutical specialization of individual Russian regions will enhance their innovation capacity and growth of the Russian economy, and the use of a breakthrough positioning strategy will form an effective pharmaceutical specialization of regions.