Based on clinical and laboratory surveillance data, trends in the incidence rates of genital Chlamydia trachomatis infections in Sweden between 1991 and 1999 were analysed according to age group and sex. The influence of changes in laboratory methods on the reported infections was assessed. After a decrease in the incidence rate of infection of 36% between 1991 and 1994, followed by a period of stability, a 20% increase was observed between 1997 and 1999 (from 157 to 189/100,000). Between 1991 and 1999 the female:male ratio decreased from 1.7 to 1.4. Incidence rates started to increase in 1994 in the 15-19 y age group for both sexes. Crude Chlamydia positivity increased from 4.1% (352,050 people tested) in 1994 to 5.4% (305,946 people tested) in 1999. This increase in Chlamydia positivity was seen both in laboratories that had changed to more sensitive methods and in those that had not. Changes in laboratory methods can therefore only partially explain the increase in notified cases. Increased screening of men may have contributed to the increase, but rising incidence rates in all young age groups of both sexes suggest a true increase in prevalence.