Dysfunction of gonadotropin-releasing hormone (GnRH) causes a range of reproductive disorders resulting from defects in the specification, migration and/or function of GnRH neurons. These phenotypes are often in association with other developmental defects such as anosmia, oligodontia, or cardiomyopathy. To identify new molecular components of this system, advanced technologies such as whole exome sequencing have accelerated the discoveries of causal genes for families with isolated or syndromic GnRH deficiency (IGD). To date, more than 20 genes have been associated with IGD explaining 40% of the cases. To determine the causality of genes and genetic variants identified by human genetic tools, functional studies utilizing animal models have been performed. For the past decade, zebrafish has emerged as a powerful, cost-efficient animal model to study genes involved in complex genetic disorders. Here, I will review few examples of how the developing zebrafish can be utilized to study GnRH dysfunction during development. This model can also become an in vivo plateform to screen small molecules with therapeutic value.