The present study evaluates the putative differences between NPFF1 and NPFF2 receptor distribution and density throughout the central nervous system between rat and mouse strains by using in vitro quantitative autoradiography. The binding of [125I]YVP ([125I]YVPNLPQRF-NH2) and [125I]EYF ([125I]EYWSLAAPQRF-NH2), used to label NPFF1 and NPFF2 receptors, respectively, was compared between Sprague-Dawley and Wistar rats and between Swiss and C57BL/6-SV129 mice. In contrast to Wistar, Sprague-Dawley brains contained NPFF1 binding sites in the cortical and spinal cord areas, the accumbens nucleus, the anterodorsal thalamic nucleus, the parafascicular thalamic nucleus, the inferior colliculus and the nucleus of the solitary tract. The distribution of NPFF2 binding sites was also different between the two strains of rats. As compared to Swiss, C57BL/6-SV129 mice showed higher basal NPFF2 receptor levels in cortical areas, telencephalon and some other regions. In contrast, they showed lower amounts in thalamic structures, except the reuniens nucleus, and in mesencephalic and rhombencephalic regions. In the cervical spinal cord the levels of NPFF2 receptors were similar. The NPFF1 binding levels were nearly the same in telencephalic structures while distinct in the forebrain. Differences in amount of NPFF receptor subtypes among these strains of rats or mice could lead to differences in NPFF control of opioid nociception.