We are performing microarray experiments for expression profiling of zebrafish embryogenesis, both as a baseline for future analysis of mutant and other conditions and to validate our microarray technology. For our purpose we used the Affymetrix zebrafish array which contains approximately 15,000 genes. This represents about 50 % of the estimated number of zebrafish genes. Total RNA was collected from embryos at 16 different stages (zygote, shield stage, 75 % epiboly, 90 % epiboly, bud stage, 5-somite stage, 14-somite stage, prim-5 stage, 32 hpf and long-pec stage, 4d post fertilization (dpf), 5 dpf, 14 dpf, 30 dpf, 90 dpf, adult). Microarray analysis was performed with these stages in single colour experiments. After normalization, differential expressed genes were selected and further analyzed with GeneSpring software. In order to validate the microarray data and to assign biological functions we chose a few genes to do semi-quantitative real-time PCR. Many of the differentially expressed genes are unknown and could be candidates for regulatory genes identified in mutagenesis experiments. We identified several genes known to be involved in zebrafish organogenesis as well as novel genes with unique temporal expression patterns.