The use of healthcare databases in research provides advantages such as increased speed, lower costs and limitation of some biases. However, database research has its own challenges as studies must be performed within the limitations of resources, which often are the product of complex healthcare systems. The primary purpose of this document is to assist in the selection and use of data resources in pharmacoepidemiology, highlighting potential limitations and recommending tested procedures. This guidance is presented as a detailed text with a checklist for quick reference and covers six areas: selection of a database, use of multiple data resources, extraction and analysis of the study population, privacy and security, quality and validation procedures and documentation.