This study assessed the age and gender distribution of Chlamydia trachomatis infections among patients attending two clinics for sexually transmitted diseases (STDs) in Slovenia. Between January 1999 and December 2003, 1714 heterosexual male and 892 heterosexual female patients were tested for C. trachomatis. The prevalence of C. trachomatis infection was 19.5% (n = 334) for male patients and 10.7% (n = 96) for female patients, with the highest prevalence in the group aged 15-30 years. The prevalence decreased between 2000 and 2003 among female patients. The results support the implementation of routine screening for C. trachomatis genital infection among male and female patients aged < 30 years attending STD clinics in Slovenia.