This paper presents an analysis and implementation of a clinical data warehouse. It focuses on the nature of health data and points out implications that arise when warehousing this data. Especially concerns in regards to data privacy and authentication, data completeness and quality are addressed. First, we explore privacy preserving methods and propose a query-time validation scheme that protects against privacy disclosure caused by combining data attributes. To enforce the access control, we propose a novel concept of composite security levels. Second, we introduce techniques and methods to overcome these issues, and suggest strategies for practical implementation. Finally, we introduce the system prototype that was developed during this project, and explain and illustrate, how these techniques and methods were applied in practice with emergency data.