Secretory immunoglobulin A (S-IgA) plays the major role for protecting mucosal tissue from infection, and its level in saliva is thought to be the indicator of immune function in the oral cavity. In the present study, we measured the levels of S-IgA, cortisol and total protein in whole saliva as well as flow rate in healthy young adults (n=8) throughout a 24-hr period, and found that salivary S-IgA, cortisol and flow rate fluctuated in a circadian manner with their acrophases (peak time of the rhythms) at 06:50h, 09:04h and 19.01h, respectively (P<0.05). Mesor (midline estimating statistics of rhythm) of the three rhythms was 0.30mg/ml for S-IgA, 8.56ng/ml for cortisol, and 0.47ml/min for the flow rate. The acrophase of S-IgA rhythm corresponded to the nadir of the flow rate rhythm, indicating that these two rhythms are anti-phase to each other. We suggest that the circadian rhythm of S-IgA is not simply subject to daily fluctuation of the volume of salivary fluid that dilutes S-IgA, but is influenced directly or indirectly by central circadian pacemaker, because the ratio of S-IgA to total protein in the morning is more than 3 times higher than that in the evening. The elevation of S-IgA concentration in saliva from midnight to early morning may indicate compensatory mechanism of oral immune system to the fall of saliva secretion during sleep.