The circadian system is a flexible framework allowing a proper adjustment of physiological functions to the regularly changing environment. Pathways that are used to synchronize components of the circadian system have been shown to be susceptible to pathophysiological conditions. In our study, we investigated effects of streptozotocin (STZ)-induced diabetes mellitus on function of the circadian system at the level of melatonin synthesis and expression of per2 and dbp in the heart and liver in 8-week-old Wistar rats. Rhythmic pattern of clock gene per2 and transcription factor dbp in controls and STZ-treated animals was determined. Streptozotocin administration had a more substantial effect on per2 expression in the liver than in the heart. Pronounced phase advance in the rhythm of dbp expression in both the liver and the heart was observed. The melatonin rhythm reflecting the phase of the master clock was not affected by STZ application. Changes in per2 and dbp expression in the heart and liver imply alterations in input pathway or peripheral oscillators with possible consequences on function of analysed organs.