Background: Atlantic cod (Gadiiformes) is an economically and culturally important species in the north Atlantic region, but early sexual maturation and variable gamete quality in brood- stock hamper development of effective cod farming. Whereas the pituitary-gonad axis has been studied for some time, information is scarce regarding the neuroendocrine regulation of puberty in cod. We therefore have initiated a research project investigating the physiology and regulation of brain GnRH systems and their impact on pituitary gonadotropes, combining molecular and electrophysiological approaches. Here, we present a molecular characterization of the different forms of GnRH and GnRH receptors (GnRH-R) in cod. Methods: Total RNA was extracted from brains and pituitaries sampled from maturing cod. A combination of RT-PCR and RACE-PCR were applied to isolate GnRH and GnRH-R cDNAs, using degenerate primers based on conserved regions from available teleost sequences. Phylogenetic analyses based on deduced amino acid sequences of the isolated cDNAs were performed using ProTest 1.3 and PHYML. mRNA expression analyses during puberty were performed using newly developed SYBR-green based qRT-PCR assays. RESULTS: The isolated GnRH ligand cDNAs each encodes a signal peptide, the GnRH decapeptide, and a GnRH-associated peptide (GAP), which is connected to GnRH by a Gly-Lys-Arg sequence. The GnRH-R cDNAs each encodes a 300–400 aa protein containing seven hydrophobic transmembrane domains and N- and C-terminal regions. Sequence and phylogenetic analyses have confirmed the identity of the isolated cDNAs. We are currently investigating the mRNA expression patterns in brain and pituitary through pubertal development. Conclusion: The isolated cDNAs provide us with important tools for further investigations on the physiology and regulation of GnRH systems in cod.