This study is an attempt to diagnose male infertility not depending only on the criteria of seminal alteration and changes in the levels of reproductive hormones but also the changes in sperm and blood cells at molecular level. The study involved one hundred and fifty infertile men and sixty fertile (control) with an average age of 20 to 60 years, who were attending the Institute of Embryo Research and infertility Treatment (ERIT) from April 2007 to March 2008. Subjects included were mostly from Baghdad province (48%) while the remaining (52%) were from other provinces: Erbil, Diayala, Ninawa, Basraha and Thi-Qar. All subjects included in this study had at least two semen analysis readings, with one measurement of reproductive hormones namely, follicle stimulating hormone (FSH), luteinizing hormone (LH), testosterone and prolactin. Pending on the out come of semen analysis of infertile men was classified into eight infertiles groups: oligoasthenoteratospermic (OAT) forming 37.3%, asthenoteratospermic (AT) 28%, and azoospermic 17.3%. The other groups: Asthenospermic (A), Teratospermic (T), Oligoasthenospermic (OA), absent ejaculation (AE) and Oligoteratospermic (OT), were found in low percentage. Results of semen analysis indicate that semen volume, seminal pH, liquefaction time and sperm agglutination were found nearly within the normal range. Moreover, most of semen samples showed infections as indicated by elevated leukocytes (WBCs) concentrations above the normal limit, with a significant change P<0.05 when infertile groups are compared with each other or with control, FSH concentration was found within the normal levels in all infertile groups, apart from azoospermic group where a significant elevation was observed when compared to the control P<0.05. Also, LH concentration was normal in all groups except for teratospermic group which showed mild reduction. Testosterone level was within the normal range in all groups. Serum prolactin concentrations were elevated above in most infertile groups, except for asthenosperaiic, oligoasthenospermic and absent ejaculation group where it was within normal range. On molecular level DNA extracted from the semen and blood and digested with methylation sensitive and insensitive restriction endonucleases Msp I and Hpa II respectively. Restriction digests were subjected to RAPD-PCR using random primer OPA-18 to determine DNA polymorphisms in 16 individuals (12 patients and 4 healthy). For the DNA extracted from blood, polymorphism percentages were relatively high in all subjects (infertile and fertile) ranging from 40-100% while DNA polymorphism extracted from semen of the same subjects showed a considerable higher range 28.57-70% with 44.99 in patients and lower range of DNA polymorphism 0.058-35.29% with 18.06 as a mean value in fertile (control) subjects. Suggesting that DNA from semen can be considered as more informative marker than DNA from blood concerning the infertility cases. Increases in DNA polymorphism with relatively steady percentage were accompanied by an increase in percentage of OAT in infertile patients ranging from 50-54%. A relatively high percentage of DNA polymorphism was observed in patients P 41, P44 with lowest level of hormone testosterone. This study which is probably the first of its kind in Iraq, focused on studying the molecular bases of infertility at the epigenetic level. It may open the door for further deep studies on infertility which is a necessary step to go further using new techniques in infertility diagnosis.