Background: Severe Toxoplasma gondii infection in early pregnancy brings the risk of transferring the infection to the unborn baby with serious abnormality. The aim of identifying toxoplasmosis in early stage is to recognize mother-to-infant transmission for early cure to avoid undesirable complication. Using serological test to determine anti-Toxoplasma specific IgG and IgM antibodies possibly may not identify new or even previous infection. However, many molecular techniques are now being extensively used through the world among these methods polymerase chain reaction PCR technique emerged as the most widely accepted method for directly detection infectious agents. Thus, the goal in this study is to compare immunoassay by indirect (IgM and IgG) detection diagnostic technique and conventional PCR as molecular assay in diagnosis of T. gondii in whole blood of aborted females in Kirkuk province-Iraq. Methods: Here we applied indirect routine serological diagnosis test for detection toxoplasma specific IgM and IgG antibodies in females blood with spontaneous abortion and compare the efficiency of this method with PCR technique to detect the pathogenic protozoan T. gondii based on identification of (the B1 gene) as a target. Eighty-one females were incorporated in this study with a history of recurrent spontaneous abortions. All of these cases were limited to only females in the reproductive age (19-44 years). There are several serological diagnostic test kits available in Iraqi markets; however, the sensitivity and effectiveness of these commercial kits are not examined by most of the laboratories before they are obtained. Therefore, blood samples from female patients with single or repeated abortion were tested for detection specific anti-Toxoplasma antibodies using commercially available (Medical-Biozec) kit in Kirkuk province and compare that with the results are obtained from conventional PCR assay. Results: The results showed that the conventional-PCR analysis is remarkably more sensitive than serological test, with a relatively high proportion of the positive samples for PCR compared with the serological diagnosis. The serological test results revealed that anti-T. gondii antibodies were detected in 14.81% of aborted women, 3.7% of them were positive for IgM, while 11.11% were positive for IgG. On the contrary, conventional PCR analysis found that 44.44% of aborted women showed positive result for B1 gene of T. gondii. Despite this, most of positive serology-aborted women exposed positive result for B1 gene of T. gondii, except two cases include false-positive IgM results.