The zebrafish is an attractive model system for a variety of applications in basic research and drug discovery because of its similarities with human disease phenotypes. Many imaging based assays have been developed to measure phenotypic changes in zebrafish, but image acquisition and analysis are tedious and time consuming when performed manually. Automation of these processes increases throughput, whilst also enhancing data quality. Here, we show how the Operetta CLS™ and Opera Phenix™ high-content analysis and screening platforms streamline imaging and phenotypic analysis of zebrafish enabling you to focus on data evaluation rather than data generation.