Daily rhythms in behavior and physiology are under control of the suprachiasmatic nucleus (SCN), the main mammalian circadian pacemaker located in the hypothalamus. The SCN communicates with the rest of the brain via various output systems. The aim of the present study was to determine the neuroanatomical and temporal relationship between two output systems, arginine-vasopressin (AVP) and transforming growth factor alpha (TGFalpha), in the mouse SCN. TGFalpha-positive cells were found throughout the SCN, but more abundantly in the core than the shell area, while AVP was predominantly found in the shell. Fluorescent double labeling revealed a total lack of co-expression for the two proteins in SCN cells. The circadian profile, studied by way of optical density in immunostaining at 3 h intervals, showed peak values for AVP shortly after the LD transitions. Immunoreactivity for TGFalpha was highly variable, especially at time points before the LD transitions. In addition, strong lateralization in TGFalpha immunostaining in the SCN was found in some individuals. Daily fluctuations in the paraventricular nucleus were absent for TGFalpha, and only weakly present for AVP. The main conclusion derived from this study is that these two output systems of the biological clock are anatomically separated with different daily profiles in expression.