The free-running rhythms of motor activity in blinded rats were measured by two different devices, an Automex or a running wheel. The period of free-running rhythm measured by a running wheel was likely to be shorter than that measured by an Automex, indicating that subtle environmental difference, such as whether a cage is equipped with a wheel or not, can affect the free-running period. In addition, we found a negative correlation not only between the free-running period measured by a running wheel and that measured by an Automex, but between the free-running period and the number of wheel revolutions per day. This is the first evidence that motor activity, other than the external factors such as light intensity and temperature, may be related to change in the free-running period.