Objective To certify that Chlamydia can spread from the genital tract to the gastrointestinal tract for long-lasting colonization. Methods Totally, 120 female C57BL/6J mice aged 5 - 6 weeks were divided into 4 experimental groups to be inoculated with purified Chlamydia muridarum (C. muridarum) elementary bodies in the vagina (n = 35) , gastric area (n = 30) , anus and rectum (n = 30) , retro-orbital venous plexus (n = 5) respectively. Moreover, corresponding negative groups inoculated with sucrose phosphate glutamate buffer (n = 5) were set up for each experimental group. On days 3, 7, and every 7 days, vaginal and rectal discharges were collected with swabs from the mice, and the number of live C. muridarum orgnisms in exfoliated cells infected with C. muridarum in the swabs was determined. Indirect immunofluorescence assay and quantitative PCR (qPCR) were performed to determine the number of live chlamydial organisms and the copy number of chlamydial genomes in the mouse genital tract (vagina, uterus, oviduct and ovary) , gastrointestinal tract (stomach, small intestine, cecum, colon, rectum) and parenteral tissues (heart, liver, spleen, lung, kidney) on days 7, 14, 28, 56 and 105 after the inoculation. The number of live chlamydial organisms and copy number of chlamydial genomes were transformed logarithmically with a base of 10. The degree of hydrosalpinx and inflammation in the genital tract, and histopathological changes of the gastrointestinal tract were observed. The infectivity and virulence of C. muridarum in the genital tract and gastrointestinal tract were evaluated in the intragastric inoculation group and intra-anal and intrarectal inoculation group on days 28 and 56 after the inoculation. Blood samples were obtained from the mouse caudal vein in the retro-orbital venous plexus inoculation group on days 3, 5, 7, 10 and 14 after the inoculation, the number of live chlamydial organisms and the copy number of chlamydial genomes in the blood samples were determined, and chlamydial infectivity in the genital tract and gastrointestinal tract was evaluated on day 56. Results On day 7 after the inoculation in the vagina, both C. muridarum live organisms and genomes were detected in the genital tract, gastrointestinal tract and parenteral tissues of all the mice. The largest common logarithm of the number of C. muridarum inclusion forming units (IFU) was observed in the vagina (6.26 ± 0.56) , with the common logarithm of the copy number of chlamydial genomes in the vagina being 7.30 ± 0.23, and the common logarithms of the number of Chlamydia IFU and genomic copy were 2.60 ± 1.95 and 4.87 ± 0.09 respectively in the rectum. On day 28, no live Chlamydia was detected in the heart, lung or other parenteral tissues, while live Chlamydia could be found in the genital tract and gastrointestinal tract. The common logarithms of the number of Chlamydia IFU and genomic copy were 3.47 ± 1.06 and 5.80 ± 1.49 respectively in the vagina, and 4.00 ± 0.35 and 5.14 ± 0.81 respectively in the rectum. On day 56, live Chlamydia could only be detected in the gastrointestinal tract. On day 105, live Chlamydia and its genomes could be still detected in the gastrointestinal tract, and the common logarithms of the number of Chlamydia IFU and genomic copy could be up to 2.60 ± 0.65 and 4.29 ± 0.57 respectively in the rectum. On days 28 and 56 after the inoculation, both live Chlamydia and its genomes could be detected in the gastrointestinal tract of all the mice in the intragastric inoculation group and intra-anal and intrarectal inoculation group. Chlamydia could survive in the blood for about 14 days in the retro-orbital venous plexus inoculation group, and live Chlamydia was detected in anal-rectal swabs in all the mice on day 14. On day 56 after the intravaginal inoculation with C. muridarum, severe hydrosalpinx, chronic inflammation and oviduct dilation occurred in the genital tract of 5 mice, but there was no obvious infiltration of inflammatory cells in the gastrointestinal tract, and inflammatory pathological changes were not observed in the gastrointestinal tract of mice after inoculation with Chlamydia through other routes either. Conclusion The infection with Chlamydia in the genital tract can lead to systemic dissemination, and Chlamydia can be spread to the gastrointestinal tract, and colonize and survive in the gastrointestinal tract for a long time. Key words: Chlamydia infections; Chlamydia trachomatis; Chlamydia muridarum; Gastrointestinal tract; Reproductive tract infections; Colonization