Development and function of the forebrain gonadotropin-releasing hormone (GnRH) neuronal system has long been the focus of study in various vertebrate species. This system is crucial for reproduction and an important model for studying tangential neuronal migration. In addition, the finding that multiple forms of GnRH exist in the CNS as well as in non-CNS tissues, coupled with the fact that GnRH fibers project to many CNS regions, implies that GnRH has a variety of functions in addition to its classic reproductive role. The study of the GnRH system and its functions is, however, limited by available model systems and methodologies. The transgenic (Tg) GnRH3:EGFP zebrafish line, in which GnRH3 neurons express EGFP, allows in vivo study of the GnRH3 system in the context of the entire animal. Coupling the use of this line with the attributes and molecular tools available in zebrafish has expanded our ability to study the forebrain GnRH system. Herein, we discuss the use of the Tg(GnRH3:EGFP) zebrafish line as a model for studying forebrain GnRH neurons, both in developing larvae and in sexually mature animals. We also discuss the potential use of this line to study regulation of GnRH3 system development.