Circadian rhythms are intrinsic, with roughly 24 h oscillations that coordinate many physiological functions and are increasingly recognized as key determinants of human health. When these rhythms become misaligned, there is an increased risk for neurodegenerative and psychiatric disorders, metabolic syndrome, sleep disturbances, and even certain cancers. The hormones, melatonin that rises in the evening and cortisol that peaks shortly after awakening, represent crucial biochemical markers of the circadian phase. This review systematically evaluates contemporary techniques for quantifying melatonin and cortisol, comparing biological matrices (blood, saliva, urine) alongside analytical platforms. Special focus is placed on two clinically informative markers: Dim Light Melatonin Onset (DLMO) and the Cortisol Awakening Response (CAR). We compared immunoassays with liquid chromatography tandem mass spectrometry (LC MS/MS), highlighting differences in sensitivity, specificity, and laboratory feasibility. Potential confounders, including ambient light, body posture, and exact sampling times-are discussed in detail, to show the capacity of providing the most reliable results. By emphasizing the need for standardized protocols and controlled sampling conditions, this review provides essential guidance for researchers and clinicians aiming to assess the circadian biomarkers melatonin and cortisol with precision since they can be used in clinical practice as diagnostic and prognostic tools for assessing numerous pathologies.