Improving the interoperability of healthcare information systems is a crucial clinical care issue involving disparate but coexisting information systems. However, healthcare organizations are also facing the dilemma of choosing the right ETL tool and architecture pattern as data warehouse enterprises. This article gives an overview of current ETL tools for healthcare data integration. In addition, we demonstrate three ETL processes for clinical data integration using different ETL tools and architecture patterns, which map data from various data sources (e.g. MEONA and ORBIS) to diverse standards (e.g. FHIR and openEHR). Depending on the project’s technical requirements, we choose our ETL tool and software architecture pattern to boost team efficiency.