Male Infertility, a problem face about 15% of non conceiving couples during their reproductive lives in the world, known to be multifactorial and there is no doubt that micro-organisms (including Chlamydia trachomatis) play a significant causative role. The demonstra¬tion of a relationship between this agent and male infertility would have important public health conse¬quences. A case control study was conducted in four infertility centers in Baghdad for a period of one year started from first of March 2007 till the end of February 2008, to determine the relationship of C. trachomatis with male infertility. Data were collected using a well designed questionnaire form, subjects were interviewed and information were collected on demographic and epidemiologic variables, medical and sexual history and smoking history for each subject and case was obtained. Different tests were applied including general semen analysis, Enzyme Linked Immunosorbent Assay, and Polymerase Chain Reaction "for the first time in Iraq". A total of 360 subjects were included in the study (180 cases and 180 controls).The age of infertile males ranged between 18-49 years with mean of 32.56±7.38 years and 32.46± 6.85 for fertile subjects. Most cases and controls were living in urban area. The current study showed that the infertile males were from varying level of education, of primary type, and were self-employed. A higher percentage (10.6%) of infertile males reported positive history of alcohol drinking than that of fertile subjects (3.3%) with a positive history of extra marital relationship (26.7%, of infertile and 8.9% of fertile). Regarding seminal fluid parameters, significant differences were found between infertile and fertile subjects in count, motility, morphology, and sperm agglutination. The current study showed that a higher percentage (29.44%) of positive IgG antibody were detected among infertile males which was statistically significant when compared to healthy controls (7.78%) A higher percentage of positive antichlamydial (IgG) antibodies were in the age group 20-29 years and they were illiterates, had positive history of alcohol drinking, extra marital relationship, with primary type infertility, and had lower percentage of positive leukocytes count when compared to the negative IgG cases.There were significant differences between positive antichlamydial IgG and some semen parameters especially grade C and sperm agglutination. Polymerase Chain Reaction was randomly applied for 50 positive antichlamydial immunoglobulin (IgG) giving a percentage of 36% in detecting C.trachomatis among infertile males. The current study showed that the highest percentage of positive Polymerase Chain Reaction test for C. trachomatis in the age group (20-29), and they were illiterates, had positive history of alcohol drinking, extra marital relationship, with primary type infertility, and had lower percentages of positive leukocytes count when compared to the negative Polymerase Chain Reaction.There were no significant differences between alcohol drinking habit, residence, smoking and semen parameters. In conclusion C. trachomatis antibodies(IgG) seem to be widespread among infertile males with higher percentage at age 20-29 years, and this organism can affect sperm motility, thus, can play possible role in the etiology of male infertility, one third of positive antichlamydial immunoglobulin (IgG) by Enzyme Linked Immunosorbent Assay test had positive, Polymerase Chain Reaction . It is recommend that screening for Chlamydia infection is to be a routine part of the work-up of the infertile couple with stressing on the role health education "including sexual education" to be applied for all sectors of the community.