Diseases caused by C. trachomatis have an adverse impact on male and female health and the reproductive function and are among the leading causes of infertility. Even though C. trachomatis is a sexually transmitted pathogen adapted to the epithelial cells of the urogenital tract (UGT), it has a fairly wide tropism and can infect blood cells, conjunctival epithelium, synovial cells, hepatocytes, and enteroendocrine cells. The pathogen is detected in various divisions of the gastrointestinal tract (GIT) in men and women. Studies of the infection in mice showed that chlamydia could spread in the body with lymph or blood flow, colonize various digestive organs, and persist in these organs for a long time without causing a significant pathology, but still inducing chronic pathological inflammation in the reproductive organs. Studies in the C. muridarum model demonstrated the role of the conservative chlamydial protein Pgp3 (encoded by the plasmid sequence) in colonization of the digestive tract. There is accumulating experimental and clinical evidence characterizing the intestine as a favorable niche for the persistence of chlamydia, since the intracellular pathogen сan avoid the competitive impact of the intestinal microflora, and immune homeostasis on the intestinal mucosa weakens the protective action of the immune response. Generalization of the urogenital chlamydial infection and colonization of the digestive tract by chlamydia are probably the main causes for the emergence of a chronic infection and the development of pathology in the reproductive sphere and other organs. If the role of this mechanism in the emergence of a chronic infection is proven, new approaches for the diagnosis and treatment of chlamydiosis will become necessary. The present review addresses these new data.