We report results of application of our endoscopic optical coherence tomography (EOCT) system in clinical experiments to image human internal organs. Based on the experience of studying more than 100 patients, we make first general conclusions on the place and capabilities of this method in diagnosing human mucous membranes. It is demonstrated that EOCT can serve for several clinical purposes such as performing directed biopsy, monitoring functional states of human body, guiding surgical and other treatments and monitoring post-operative recovery processes. We show that applications of OCT are more informative in the case of internal organs covered by epithelium separated from underlying stroma by a smooth basal membrane and therefore concentrate on the results of the EOCT study of three internal organs, namely of larynx, bladder, and uterine cervix. Finally, we report first examination of internal organs in abdomen with the use of laparoscopic OCT.