Background: Rather little is known about the late sequelae of previously detected female Chlamydia infections. Methods: The late sequelae of previous female Chlamydia infections detected during a 15-year period in a south-western Finnish university hospital were surveyed. Hospital records of women with positive laboratory diagnoses of Chlamydia trachomatis as a sign of genital infection were collected from the years 1990–2006 and subsequently linked to known or suspected in-hospital-treated late Chlamydia complications. Results: The annual number of late complications has increased in proportion to the increasing trend of detected Chlamydia cases. 239 late complications of the total of 4,920 previously detected Chlamydia-positive infections were observed. The most frequent in-hospital-treated complications were disturbances in early pregnancy (n = 72) and low abdominal pain (n = 67). The others were 45 genital tract or pelvic infections, 34 cases of tubal or unknown infertility and 21 complications of late pregnancy and delivery. Conclusion: The late sequelae of Chlamydia infections need increasing attention in hospitals.