The huge increases in medical devices and clinical applications which generate enormous data have raised a big issue in managing, processing, and mining this massive amount of data. Indeed, traditional data warehousing frameworks can not be effective when managing the volume, variety, and velocity of current medical applications. As a result, several data warehouses face many issues over medical data and many challenges need to be addressed. New solutions have emerged and Hadoop is one of the best examples, it can be used to process these streams of medical data. However, without an efficient system design and architecture, these performances will not be significant and valuable for medical managers. In this paper, we provide a short review of the literature about research issues of traditional data warehouses and we present some important Hadoop-based data warehouses. In addition, a Hadoop-based architecture and a conceptual data model for designing medical Big Data warehouse are given. In our case study, we provide implementation detail of big data warehouse based on the proposed architecture and data model in the Apache Hadoop platform to ensure an optimal allocation of health resources.