In the present study, a model for the human gonadotropin-releasing hormone receptor embedded in an explicit lipid bilayer was developed. The final conformation was obtained by extensive molecular dynamics simulations of a homology model based on the bovine rhodopsin crystal structure. The analysis of the receptor structure allowed us to detect a number of specific contacts between different amino acid residues, as well as water- and lipid-mediated interactions. These interactions were stable in six additional independent 35 ns long simulations at 310 and 323 K, which used the refined model as the starting structure. All loops, particularly the extracellular loop 2 and the intracellular loop 3, exhibited high fluctuations, whereas the transmembrane helices were more static. Although other models of this receptor have been previously developed, none of them have been subjected to extensive molecular dynamics simulations, and no other three-dimensional structure is publicly available. Our results suggest that the presence of ions as well as explicit solvent and lipid molecules are critical for the structure of membrane protein models, and that molecular dynamics simulations are certainly useful for their refinement.