OBJECTIVES: To organize and classify existing Canadian health information databases into a searchable repository that will assist in identifying and assessing Canadian data available for health outcomes and related research. METHODS: The identification of Canadian health information databases began with a structured search strategy involving Medline (PubMed, OVID); Internet search engines; web sites of a number of organizations, universities and government bodies; and personal communications. Canadian databases with data from the year 2000 and onwards were included. Databases were assigned to one of four basic types (Administrative, Registry, Surveillance and Survey) and further classified in a hierarchical structure using categories, sub-categories and low-level terms. The three high-level categories were Medical Condition (MC), Population Health (PH) and Health Services Utilization (HSU). Approximately 20% of the identified databases were further profiled in detail, with recording of information on an additional 20 variable fields including sample size, data collection methods and data quality. RESULTS: The creation of a classification structure fully characterized the breadth and scope of the 255 unique databases initially identified. By database type, the largest proportion of databases was classified as survey (34%; n=87), followed by administrative (28%; n=72), registry (22%; n=56) and finally surveillance (16%; n=40). By non-exclusive database category, most were classified as PH (n=140), followed by HSU (n=116) and finally MC (n=114). Canadian health databases were found to provide information across a wide range of clinical conditions, particularly those related to high disease burden areas. In addition, they provided health utilization and determinant data. Some data gaps were recognized, such as environmental exposure data, data identifying specific subpopulations, and information needed to fully assess data quality. CONCLUSIONS: Classifying existing Canadian health information databases within a single, organized register is expected to provide an effective research tool in the planning of health outcomes and related research.