Chlamydia trachomatis is the most common bacterial sexually transmitted infection in Europe and has large impacts on patients’ physical and emotional health. Unidentified asymptomatic rectal Chlamydia trachomatis could be a partial explanation for the high Chlamydia trachomatis prevalence. In this study, we evaluated rectal Chlamydia trachomatis testing in relation to symptoms and sexual habits in women and men who have sex with men. Rectal Chlamydia trachomatis prevalence was 9.1% in women and 0.9% in men who have sex with men. None of the patients reported any rectal symptoms; 59.0% of the women with a rectal Chlamydia trachomatis infection denied anal intercourse and 18.8% did not have a urogenital infection; 9.4% did neither have a urogenital infection nor reported anal sex. We suggest that rectal sampling should be considered in women visiting sexually transmitted infection clinics regardless of rectal symptoms and irrespective of anal intercourse, since our data suggest that several cases of rectal Chlamydia trachomatis otherwise would be missed, thus enabling further disease transmission.