Objectives. - To determine the frequency of Chlamydia trachomatis genital infection within sexual partnerships using highly sensitive polymerase chain reaction (PCR) amplification and to identify the variables that might modify transmission. Design. - Cross-sectional study of sexual partnerships comparing in vitro culture and PCR amplification for C trachomatis. Setting. - Two outpatient sexually transmitted disease clinics. Participants. - Four hundred ninety-four people in sexual partnerships attending sexually transmitted disease clinics. Main Outcome Measures. - Genital infection with C trachomatis. Methods. - DNA sequencing was performed to examine specific genotypes within and between partnerships. Cross- sectional analysis was performed to determine characteristics associated with concordance or discordance of infection with partnerships. Results. - Cultures were positive for C trachomatis in 8.5% of males and 12.9% of females (P=.03). Using PCR, more infections were identified both in males (14.2%) and in females (15.8%), and the difference in infection rates analyzed by sex was no longer significant. In 20.4% of 494 couples, at least 1 partner had PCR results positive for C trachomatis, with a concordant infection rate of 10.7%, significantly higher than the 5.5% concordant infection rate demonstrable by culture (P<.01). Male-female and female-male transmission frequencies were equal (68%). The nucleotide sequences of the major outer membrane protein gene products were identical and unique for each of 15 culture-negative, PCR-positive concordant partnerships. In concordant infections, factors associated with infection in female partners were age less than 20 years, more than 1 partner in the past 6 months, and cervical ectopy greater than 25%. Conclusions. - Using PCR, the frequency of chlamydia transmission by infected males and females was nearly identical. The high rate of concordant infection, high frequency of infection among asymptomatic individuals, and high frequency of transmission regardless of sex underscore the importance of routine screening for chlamydia in both males and females, along with provision of treatment to all sexual partners of chlamydia- infected individuals.