The molecular clock machinery in mammals consists of a number of clock genes (CGs) and their resultant proteins that form interlocking transcription‐translation feedback loops. These loops generate and maintain the 24 h mRNA and protein oscillations and consequential biological and physiological rhythms. To understand whether peripheral oscillators share similarly‐timed clock machinery, the temporal expression patterns of the seven recognized key CGs (mPer1, mPer2, mCry1, mCry2, mRev‐erb alpha, mClock, and mBmal1) were examined simultaneously in six peripheral tissues in mice every 4 h for 24 h in synchronized light‐dark conditions using real time PCR assays. Time series were analyzed for time‐effect by ANOVA and for rhythm characteristics by the single cosinor fitting procedure. The expression levels of most CGs were comparable in liver, kidney, and spleen, but mBmal1 and mCry1 were more abundant in the thymus, and mPer1, mCry1, and mCry2 were more abundant in the testis. In addition, mCry2 was dramatically lower in the kidney, spleen, and thymus; mPer2 was significantly lower in the spleen, testis, and thymus; and all of the genes tested were strikingly less abundant in peripheral blood. A significant 24 h rhythmic component was found for each CG in the liver and kidney and for some CGs in other tissues. Of note, a 12 h ultradian rhythmic component was also found in mRNA expression for some CGs in several of the tissues and was the only significant oscillation observed for CGs in the testis. Ultradian oscillations were also observed for mPer1 in the testis (8 h) and thymus (12 h and 8 h) in a second study where mice were sampled every 2 h. The present results suggest that the functioning of the molecular circadian clock may be modified to some extent between peripheral tissues, as denoted by differences in amplitude and phasing, and operates differently or is less developed in tissues containing differentiating cells (i.e., testis and thymus), as denoted by the presence of ultradian patterns resulting in two or more peaks within 24 h.