Gastrointestinal hormones are peptides, and the gastrointestinal tract is the largest endocrine organ in the body for production of peptide hormones. As a premise for accurate measurement of gastrointestinal hormones, the present review provides first an overview over the complex biology of the hormones: The structures and structural homologies; biogenetic aspects; phenotype variabilities; and cellular expression in- and outside the digestive tract. Second, the different methodological principles for measurement are discussed: Bioassay, radioimmunoassay (RIA), enzyme-linked immunosorbent assay (ELISA), mass-spectrometry (LC–MS/MS) and processing-independent analysis (PIA). Third, the variability of secretion patterns for some of the gut hormones is illustrated. Finally, the diagnostic value of gut hormone measurement is discussed. The review concludes that measurement of gastrointestinal peptide hormones is relevant not only for examination of digestive functions and diseases, but also for extra-intestinal functions. Moreover, it concludes that, so far, immunoassay technologies (RIA and ELISA) in modernized forms are still the most feasible for accurate measurements of gastrointestinal hormones in biological fluids. Mass-spectrometry technologies are promising, but still too insensitive and expensive.