Free-running period of blinded rats kept in a cage with a running wheel varied markedly, while it varied little in rats kept in a cage without a running wheel. The mean free-running period of the former group is significantly shorter than that of the latter. In the former, the free-running period correlated negatively with motor activity, indicating that activity affects the free-running period. In both groups, essentially similar diurnal patterns of biogenic amines and their metabolites were observed in various discrete areas in the brain examined. However, there was a significant difference between the two groups in several areas. In the SCN, 5-HT content correlated positively with motor activity, consequently correlated negatively to the free-running period at 3 out of 4 sampling times over 24 h but no such correlation was observed in other monoamines and their metabolites examined. These facts suggest that 5-HT may be associated with modification of the free-running period.