The presence of reactive oxygen/nitrogen species (ROS/RNS) has been linked with both beneficial and harmful effects in living organisms. In order to study the role of ROS/RNS in health and disease states, there is a need to develop methods to quantify reactive species at the production site in live biological models. However, the detection of oxidative/nitrosative stress markers is a great challenge due to their low concentration, high reactivity, and short life-time. Zebrafish (Danio rerio) embryos are a powerful biological model for disease modeling and developmental studies. In this presentation we describe the development and use of electrochemical microelectrodes that allow for in vivo detection of ROS/RNS at single organ level in embryonic zebrafish, with a specific example for detection of nitric oxide (NO) as a representative nitrosative stress marker. Customized carbon fiber microelectrodes were used to assess the spatial distribution of NO along the intestine of zebrafish embryos. The electrochemical measurements were cross-validated by the use of fluorescence imaging and NO-specific pharmacological manipulations. These studies contribute to a better understanding of the role of ROS/RNS in a model of inflammatory intestinal disease.