Circadian rhythms, near-24 h oscillations that reflect homeostatic control by an internal timing system rather than the influence of external factors, are an important and sometimes underappreciated aspect of human physiology and biochemistry. Over the past few decades, the pineal gland hormone melatonin has been established both as a robust marker of circadian phase in plasma or saliva and as a chronobiotic drug administered to reset the timing of the circadian oscillator. Recent work by our own and other laboratories has sought to systematically investigate whole categories of molecular components in blood samples in a hypothesis-free fashion by employing metabolomic methodologies to study low molecular weight compounds and transcriptomic methodologies to study gene expression in white blood cells, respectively. A number of components have been pinpointed that show a rhythmic circadian variation or are affected by imposed factors such as sleep deprivation. Although melatonin, a robust and reliable circadian phase marker, will be a hard act to follow, these lines of research suggest numerous potential leads for useful new markers of biological timing.