Objective Chlamydia trachomatis infection is the most common sexually transmitted disease. The aim of this research is to set a standard system for determination of chlamydia load in tissues from infected animals． Methods Chlamydia trachomatis ( serovar E) was amplified in vitro for infection． The gene fragment of the chlamydia-specific gene OMP1 was cloned as standard． The quantity of chlamydia was determined based on the copy number of chlamydia genome by real time PCR． Results The results of real time PCR were linear when the copy number of OMP1 gene was within the range from 200 to 2 × 108． Unspecific amplification was not detected after adding mouse genome into the templates，nor was the amplification efficiency affected． Conclusion Real time PCR targeting chlamydia-specific gene OMP1 could be applied as a standard method to quantitatively analysis chlamydia in infected animal sample with adequate sensitivity and specificity．