Health systems around the world are moving to use health data sources to improve the efficiency of their services. However, major technical and legal questions exist concerning data integration, data quality, data security and privacy in health data usage. In this paper, we discuss the Health Data Integration™ (HDI™) solution currently being developed at the e-Health Research Centre. Firstly we describe the architecture of HDF™ and how it performs the tasks of knowledge based medical system. We then consider two of its core capabilities (1) privacy-preserving similarity linkage, and (2) on-line analytical techniques and report generator component. The e-Health Research Centre is currently working with the Queensland Health department to deploy the software in practice.