In Vietnam, it is estimated annually that more than one million new cases of sexually transmitted diseases, which are mainly caused by Chlamydia trachomatis. The molecular biological methods allow accurate determination of C. trachomatis with high sensitivity and high specificity, short-time testing and early detection of disease in the initial stage. With 10 samples tested negative for C. trachomatis (used as the template for negative control) and 36 samples collected at the Central Military Hospital No.108, the authors carried out DNA extraction by chelex process conducted by a quick, simple and safe for operations and lower costs. Then, DNA quality control and detection for C. trachoma tis using specific primers showed that 13/36 samples positive for C. trachomatis with sensitivity equivalent to a number of processes have been commercialized.Thus, the DNA extraction by chelex method can completely be used to extract DNA for use in diagnosing C. trachomatis. Also, with the sequencing techniques, we detected type C. trachomatis isolated from patients of Vietnam is 99 percent homologous with the serovar F, strain Sweden 5. This is the strain caused the disease in Sweden within two years from 2006 to 2008.