Exfoliation is a loss of cellular material retaining the basic cytological features of typical cells (plasma membrane, cytoplasm and nucleus). However, the set of physiological parameters leading to exfoliation is complex and difficult to measure. Exfoliated epithelial cells can be obtained from a wide range of mucosa like mammary glands, oral mucosa by scraping, bronchial mucosa by expectoration and gastric or colonic epithelia by extensive rinsings during routine procedures of endoscopic examination. From an histological point of view, epithelia are organized in functional units containing different cellular compartments (stem, proliferative, mature or functional and senescent cells). Exfoliation is either (I) a natural loss of body cells implying a molecular signal related to the turn-over of terminally differentiated cells and to the progressive mobilization of proliferative as well as stem cells or (2) the result of manual exfoliation by applying mechanical constraints like gentle swabbing or scraping. Exfoliated epithelial cells are believed to be either in apoptosis or in anoikis. In the latter group, cells may survive by autophagy retaining their growth potential if proper matrix is rapidly provided after exfoliation. Most studies are based on cytological proof using microscopic examination along with a limited number of biomarkers. Only few studies using proteomics or transcriptomics are available and they open discussion about tissue references and normalization. Exfoliated cells may represent valuable source of information on the physiopathological status of the mucosa. In translational research, ethical reasons as well as legal ones are limiting the use of biopsies in favor of measures realized on epithelial cells isolated from biological fluids (milk, urines, gastric aspirates, stools) collected by way of non-invasive technology. Unambiguous knowledge on the advantages and the limitations of exfoliation methodologies could have far reaching impact on chrononutrition or chronopharmacology.