OBJECTIVES: To study the prevalence, symptoms, and signs of Mycoplasma genitalium and Chlamydia trachomatis infections in women attending a Swedish STD clinic, accessible for both sexes, and in a group of young women called in the cervical cancer screening programme. METHODS: A cross sectional study among female STD clinic attendees in Orebro and a study among women called for Papanicolaou smear screening. Attendees were examined for urethritis and cervicitis. First void urine and endocervical samples were tested for M genitalium and C trachomatis. RESULTS: The prevalence of C trachomatis and M genitalium in the STD clinic population was 10% (45/465) and 6% (26/461), respectively. Dual infection was diagnosed in four women. In the cancer screening group of women the corresponding prevalence was 2% (1/59) and 0%, respectively. Among the STD clinic attendees there were no significant differences in symptoms (32% v 23%, RR 1.4, 95% CI 0.6 to 3.4) or signs (71% v 50%, RR 1.4, 95% CI 0.9 to 2.3) between C trachomatis and M genitalium infections. Microscopic signs of cervicitis were significantly more common among M genitalium and C trachomatis infected women than in the cancer screening group of women. 56% (15/27) of male partners of M genitalium infected women were infected with M genitalium compared to 59% of male partners of C trachomatis infected women who were infected with C trachomatis (p = 0.80). CONCLUSIONS: M genitalium is a common infection associated with cervicitis and with a high prevalence of infected sexual partners supporting its role as a cause of sexually transmitted infection.