An improved nucleic acid amplification test (NAAT) to detect Chlamydia trachomatis infections, based on PCR amplification within its cryptic plasmid (CT1/CT2 Test) was developed. DNA was extracted from urogenital swabs and a 594-bp long DNA fragment from the cryptic plasmid (pCT) was amplified. The sensitivity and specificity of the CT1/CT2 Test were determined to be 100 and 99 %, respectively, when directly compared with current amplification kit for sexually transmitted diseases (MPCR). Basic epidemiological data related to the patients attending gynecological and/or urological clinics are also provided. The overall prevalence rate in this group of patients suspected for C. trachomatis infection was determined to be about 95 per 1000 (88 and 107 per 1000 in females and males, respectively). It demonstrates that the CT1/CT2 Test is suitable for epidemiological screening and/or diagnostic practice.