In this paper, we present an overview of the problems associated with the analysis and security of medical data and offer a solution that will provide the basis for improving the quality of medical services. We propose the architecture of a decentralized health data ecosystem based on a blockchain that will allow us to operate with vast volumes of clinical data, while also protecting confidential medical data. An example of a blockchain solution based on Exonum framework for state-scale use in healthcare is discussed. The deployments of such systems will the benefit to medical data safety, extend the base of clinical data collections, and create an effective shared health infrastructure.