Danio rerio are an important model system, ideal for use in many developmental, cellular, and molecular biology experiments. As use of this highly tractable model organism increases, so do the needs for more effective and efficient methods regarding their use. Homogenization is commonly used for extraction of proteins, nucleic acids, and chemical analytes from tissue or whole organisms. Here we describe a protocol for highly consistent, high-throughput homogenization of whole or dissected larval or embryonic zebrafish. Twenty-four D. rerio samples may be homogenized in a total time of five minutes.