Disturbance of clock gene expression rhythms is a risk factor for diseases such as obesity. To understand the mechanism of regulating clock gene expression rhythms in vivo, multiple real time recording systems are required. In present studies, we show micro PMT system detect Per1 gene expression rhythm over 1000 times comparing with the tissue contact optical sensor system as we report previously. Per1 expression rhythm in the back skin of freely moving mouse had a peak at CT12. At this time point, we found high Per1 expression in whole hair root tissue using micro PMT system in STZ diabetes mouse. Elevated Per1 expression by STZ administration was observed on day 2 when blood glucose content was around 400 mg/dl, which corresponds with the time of onset of severe diabetes. In contrast, scalp hair showed elevated Per1 expression on day 1 when blood glucose was still low in non-diabetic condition. A drastic increase of Per1 expression on day 1 is consistent with that of the olfactory bulb, cortex, and liver in our previous reports. These results show that our μPMT system responds to minute changes in gene expression in freely moving mice in vivo and in mice hair follicles in vitro. Furthermore, Per1 in the hair can be used for a marker of diabetic aggravation.