Membrane transporters are expressed in various bodily tissues and play essential roles in the homeostasis of endogenous substances and the absortion, distribution and/or excretion of xenobiotics. For transporter assays, radioisotope-labeled compounds have been mainly used. However, commercially available radioisotopelabeled compounds are limited in number and relatively expensive. Chromatographic analyses such as high-performance liquid chromatography with ultraviolet absorptiometry and liquid chromatography with tandem mass spectrometry have also been applied for transport assays. To elucidate the transport properties of endogenous substrates, although there is no difficulty in performing assays using radioisotope-labeled probes, the endogenous background and the metabolism of the compound after its translocation across cell membranes must be considered when the intact compound is assayed. In this review, the current state of knowledge about the transport of endogenous substrates via membrane transporters as determined by chromatographic techniques is summarized. Chromatographic techniques have contributed to our understanding of the transport of endogenous substances including amino acids, catecholamines, bile acids, prostanoids and uremic toxins via membrane transporters.