We investigated a group of male patients with idiopathic infertility to determine the presence of genital infection and to identify the pattern of this infection using a specially designed protocol. A prospective study was carried out on 63 patients and 23 controls. We cultured the first voided urine, semen and swabs taken from the anterior urethra of these patients and controls for bacteria, chlamydia. Ureaplasma urealyticum and Mycoplasma hominis. Two techniques were used for chlamydial isolation and identification. These involved the use of chlamydial culture on McCoy cells with culture confirmation test and the direct fluorescent identification of Chlamydiatrachomatis. The all-liquid media (MYCOFAST ALL-IN) kits were used for the identification of mycoplasma. Our results indicate that there is a significantly higher incidence of genital infection among male patients with idiopathic infertility than in normal fertile controls (P=0.0004). Extensive microbial investigations are indicated when genital infection is suspected to be the cause of the fertile state or cannot be ruled out as a possible cause in case of idiopathic infertility.