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. To determine the frequency of C. trachomatis Infection among infertile men with leukocytospermia using different diagnostic techniques such as the detection of secretory IgA antibodies (Abs) in seminal plasma by enzyme-linked immunosorbent assay (ELISA), plasmid DNA by polymerase chain reaction (PCR) and direct detection of elementary body by flowcytometric analysis in seminal fluid. To assess the relationship between C. trachomatis infection and semen quality hence male infertility. Seventy five infertile male patients with leukocytospermia and 25 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 secretory IgA in seminal plasma by ELISA and detection of plasmid DNA by PCR and elementary body by flowcytometric analysis in semen samples were performed. Primary and secondary infertility were detected in 55 (73.3%) and 20 (26.7%) 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 10(6)/ml was statistically significant lower than those with pus cells less than 2 x 10(6) /ml. ELISA-detected IgA Abs against C. trachomatis in patients seminal plasma were positive in 20 (26.7%) and equivocal in 5 (6.6%) patients. Flowcytometric analysis of semen sample for C. trachomatis was positive in 35 (46.6%) patients and C. trachomatis plasmid DNA detection by PCR was positive in 23 (30.7%) patients. In conclusions, Detection of C. trachomatis antibodies of IgA type by ELISA in seminal plasma appears to be as specific as PCR in diagnosis of C. trachomatis in seminal fluid. High detection rate of C. trachomatis by flowcytometry 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.