Objectives: Little is known about rectal Chlamydia trachomatis (CT) infection in outpatients attending sexually transmitted disease (STD) clinics in China. In this study, we aimed to explore the clinical and epidemiologic features of rectal CT infection in this population. Methods: A cross-sectional study which was conducted among these patients in Tianjin (northern China) and Guangxi (southern China) from June 2018 to August 2020. Bidirectionally sequences were used to analyze CT ompA genotype. Univariate and multivariate logistic regression analysis were developed to explore the association of different risk factors for urogenital and rectal CT infection. Results: A total of 1,382 patients were included in the final analyses. The prevalence of urogenital and rectal CT was 11.2% (154/1374) and 4.9% (68/1377) respectively. The rectal CT prevalence among female and male patients was 7.8% (60/767) and 1.3% (8/610) respectively. The three most common genotypes in urogenital CT samples were genotype E (41/137, 29.9%), J (27/137, 19.7%) and D (21/137, 15.3%), while the most common genotypes among rectal CT positive samples were genotype J (11/47, 23.4%), E (10/47, 21.3%) and D (9/47, 19.2%). More than 85% (52/60) of women infected with rectal CT were co-infected with urogenital CT. About 90.0% (36/40) of women shared the same genotype with urogenital samples. Age under 25 and infected NG were selected as risk factors for urogenital CT, while female patients and patients infected with urogenital CT were the risk factors for rectal CT infection. High proportion of rectal CT infection had concurrent urogenital CT infection especially in women, and most of the co-infections were shared among the same genotypes. Conclusions: It would be prudent to encourage awareness, introduce detections tests and treatment strategies for rectal CT infection particularly in female patients visiting STD clinics in China, irrespective of presence of rectal symptoms and history of anal intercourse. Funding Information: This work was supported by the Chinese Academy of Medical Sciences Initiative for Innovative Medicine (grant 2016-I2M-3-021). Declaration of Interests: The authors report no conflicts of interest in this work. Ethics Approval Statement: This study was conducted in accordance with the Declaration of Helsinki, reviewed and approved by the Institutional Review Board of the Institute of Dermatology, the Chinese Academy of Medical Sciences and Peking Union Medical College (approval number 2017-LS-021).