S-20098 is a potent nonindolic melatonin agonist that has been shown to entrain free-running circadian rhythms. The current experiments examined the role of the suprachiasmatic nuclei (SCN) and of the pineal gland in the entrainment of circadian rhythms by S-20098. First, daily injections of S-20098 (1 and 10 mg/kg s.c.) were administered to SCN- and sham-lesioned rats. At both dose levels, circadian effects were noted in all sham-lesioned animals. Locomotor activity and body temperature rhythms in 3 of 5 sham-lesioned rats were entrained by the daily injections. In SCN-lesioned rats, S-20098 had no synchronizing or entraining effects at either dose level. These results show that S-20098 exerts its entraining effects on circadian rhythms via the circadian pacemaker located in the SCN. Second, the effects of daily injections of S-20098 (10 mg/kg s.c.) were examined in pinealectomized, sham-pinealectomized, and intact rats. All rats receiving S-20098, irrespective of surgical treatment, showed circadian changes. Rhythms in 81% of these animals entrained to daily administration of the compound, indicating that entrainment induced by S-20098 does not depend on an intact pineal. When injected with 10 mg/kg S-20098, 69% of rats, irrespective of surgical treatment, showed long-term modifications of free-running period that still were evident several weeks after administration ceased. If confirmed, this finding may have therapeutic implications in humans regarding the optimal mode and administration of S-20098 in a clinical setting.