Chlamydia trachomatis infection is considered to be one of the most common sexually transmitted diseases. It is currently unclear whether chlamydial infection causes pathological conditions of the male accessory glands has consequences for male infertility. This study was aimed to determine the frequency of C. trachomatis infection among infertile men with leukocytospermia using polymerase chain reaction (PCR) and direct detection by flowcytometric analysis in seminal fluid and to assess the relationship between C. trachomatis infection and semen quality hence male infertility. One hundred infertile male patients with leukocytospermia and 30 apparently healthy age matched fertile men were included as controls. Routine semen analysis and LeucoScreen test were done for each patient and control. Detection of C. trachomatis plasmid DNA by PCR and by flowcytometric analysis in semen samples were performed. Primary and secondary infertility were detected in 72(72 %) and 28 (28%) of patients, respectively. Sperm concentration and sperm motility (A+B) were statistically significant lower in patients with leucocytospermia than control group (P<0.0001). Sperm concentration in patients with pus cells more than 3 x 106/ml was statistically significant lower than those with pus cells less than 2x106 /ml. Flowcytometric analysis of semen sample for C. trachomatis was positive in 45(45%) patients and C. trachomatis plasmid DNA detection by PCR was positive in 33 (33%) patients. In conclusions, higher detection rate of C. trachomatis by flowcytometry in comparison to was observed. Concerning the effect of C. trachomatis on routine semen characteristics, no significant obvious changes could be detected. Further studies for the assessment of sperm viability and DNA integrity are recommended.