In humans and rat, orexins orchestrate divergent actions through their G-protein coupled receptors, orexin-1 (OX1R) and orexin-2 (OX2R). Orexins also play an important physiological role in mouse, but the receptors through which they function are not characterized. To characterize the physiological role(s) of orexins in the mouse, we cloned and characterized the mouse orexin receptor(s), mOX1R and mOX2R, using Rapid Amplification of cDNA (mouse brain) Ends (RACE), RT-PCR and gene structure analysis. The mOX1R cDNA encodes a 416 amino acid receptor. We have identified two alternative C-terminus splice variants of the mOX2R; mOX2R (443 aa) and mOX2R (460 aa). Binding studies in HEK-293 cells transfected with mOX1R, mOX2R and the mOX2R revealed specific, saturable sites for both orexin-A and -B. Activation of these receptors by orexins induced inositol triphosphates (IP₃) turnover. However, HEK-293 cells transfected with mOXRs demonstrated no cAMP response to either orexin-A or orexin-B challenge, although forskolin and GTPS revealed a dose-dependent increase in cAMP. Although, orexin-A and orexin-B showed no difference in binding characteristics between the splice variants, interestingly, orexin-B led to an increase in IP₃ production at all concentrations in the mOX2R variant. Orexin-A however, showed no difference in IP₃ production between the two variants. Additionally, in the mouse, we demonstrate that these splice variants are distributed in a tissue specific manner, where OX2R mRNA was undetectable in skeletal muscle and kidney. Moreover, food deprivation led to a greater increase in hypothalamic mOX2R gene expression, compared with both mOX1R and mOX2R. This potentially implicates a fundamental physiological role for these splice variants.