The actions of intracranial injections of alpha bungarotoxin (BTX) on locomotor activity rhythms were examined in male rats. The hypothalamic suprachiasmatic region is known to be a locus of high affinity BTX binding although the potential roles of this receptor system are unknown. Rats were stereotaxically implanted with cannulae aimed just dorsal to the SCN (or cortex for control injections). Free-running locomotor activity rhythms in darkness were constantly monitored. Seventy-eight percent (78%) of the animals injected with BTX in the SCN region had phase shifts that were outside the 99% confidence limits of control animals. Infusion of either saline (into the SCN) or BTX into cortex were without effects. Doses of BTX varied from 125 fmol to 600 pmol. At the highest dose a substantial fraction of the animals showed both period changes and loss of rhythmicity as well as phase shifts. Although nearly all of the animals injected with BTX experienced phase shifts the direction of the shifts were not consistently correlated with the circadian time of injection. However, the sensitivity of the animals varied systematically with the smallest shifts resulting after injection at CT12 and CT16. These results argue that BTX does not influence the SCN pacemaker as an entraining signal but does potently perturb the circadian system.