Screening for Chlamydia trachomatis in women is generally done using only one specimen from each patient in order to minimize costs. In this study the aim was to compare the performances of vaginal, cervical and urinary specimens in a population of young women with sparse symptoms. During 1998, specimens from 1,001 women at the Departments of Venereology and Youth Health Care at the University Hospital of Uppsala, Sweden were examined by both ligase chain reaction and cell culture for detection of C. trachomatis. The samples from the cervix, vagina and urine were tested by ligase chain reaction, while specimens for cell culture were collected from the cervix and urethra. The prevalence of genital C. trachomatis infections was 5.1%. A single urine specimen had a sensitivity of 80.0%, while the sensitivity of a single vaginal specimen was 96.0%. The specificity was 100% for the urine specimens and 99.4% for the vaginal specimens. The sensitivity and specificity of a single cervical specimen was 92.0% and 99.6%, respectively. Although the urine ligase chain reaction seemed to have the lowest sensitivity of the compared specimens for testing of C. trachomatis infections in this population, the differences in sensitivity between urine, cervical and vaginal specimens were not statistically significant.