Most individuals infected with chlamydia remain asymptomatic, with only an estimated 10% of infected males showing symptoms and 5-30% of infected females. C. trachomatis initially infects the cervix of females and sometimes the urethra. In symptomatic females, this can result in abnormal vaginal discharge, endocervical bleeding, increased urinary frequency, and dysuria.

Symptomatic males generally develop urethritis resulting in urethral discharge, dysuria, and testicular pain. Chlamydia infections of the rectum may lead to rectal pain, discharge and/or bleeding. Sexually acquired chlamydial conjunctivitis can also occur in both males and females.