Cytochrome P450 enzymes (CYPs) are heme thiolate proteins essential for vertebrate development and also play important roles in toxicology as well as normal metabolic function. CYP enzymes catalyze the oxidative biotransformation of many endogenous and exogenous chemicals, including steroids and eicosanoids, and drugs and other xenobiotic toxicants. Many CYPs have known for their potential roles in development, and many chemicals that cause developmental abnormalities are substrates for CYPs. The roles and regulation of most xenobiotic metabolizing CYPs during development are unknown, impeding understanding of mechanisms of developmental toxicity. The zebrafish (Danio rerio) has become one of the premier models in vertebrate developmental biology, in large part because of the logistical advantages of rapid external development, high adult maintenance density, and significant (bio)technological tool availability. The increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of CYP gene regulation and function. Here, we present methods to examine CYP expression during early development in zebrafish, with an emphasis on developmental microarrays.