Aim of this paper is to propose a methodology to design Extract, Transform and Load (ETL) tools in a clinical data warehouse architecture based on the Electronic Healthcare Record (EHR). This approach takes advantages on the use of this infrastructure as one of the main source of information to feed the data warehouse, taking also into account that clinical documents produced by heterogeneous legacy systems are structured using the HL7 CDA standard. This paper describes the main activities to be performed to map the information collected in the different types of document with the dimensional model primitives.