Background: Chlamydia trachomatis infection is the most commonly reported sexually transmitted bacterial infection worldwide. Between 70 and 90% of women are asymptomatic, however, untreated and persistent infections can lead to the development of urethritis, pelvic inflammatory disease, infertility and ectopic pregnancy. Aims: To determine C. trachomatis infection frequency in a group of women in Chile, using quantitative real time PCR (qPCR) and to compare the usefulness of endocervical and urine samples for C. trachomatis detection. Methods: 87 asymptomatic women aged 15-64 years were included. Every woman donated one endocervical sample and one urine sample. Detection and quantification of C. trachomatis was performed by qPCR. Results: Of 87 endocervical samples, the frequency was 11.49% (n = 10). Of these samples, 5 cases were found in women <35 years old. About urine samples, 16 samples were positive (18.39%). Ten women <35 years old yielded positive urine samples. Only four women had both samples positive for C. trachomatis (4.6%). There was no statistically significant relationship between age and C. trachomatis infection. Cryptic plasmid quantification was found between 3.55 - 96.050 copies/mu L for endocervical samples and 7.22-633.1 copies/mu L for urine samples. Conclusion: Estimated frequency of C. trachomatis in Chilean women was higher than previous Chilean studies. Both types of samples are complementary for screening and diagnosis strategies using sensitive techniques, because silent infection can be present in either urinary or genital tract or in both in women.