Background: The PCR-based techniques detect Toxoplasma gondii DNA in patients’ samples. Real-time PCR is used mainly to quantify infection agents especially in immunecompromised cases. The aim of our study was to examine the probable association of toxoplasmosis and appendectomy in an Iranian sample of women undergone a recent abortion by the performance of real-time PCR.Methods: Sixty five abortion cases were occurred from March 2008 to October 2009 in Isfahan, Iran. Specimens from their products of conception were screened for T. gondii DNA by both the conventional PCR and real-time PCR. The acquired data was assessed in relation to the history of appendices by the statistical methods in SPSS software.Results: The results of the conventional PCR were positive in 10 (15.48%) of 65 patients and negative in 55 (84.6%). After the conventional PCR, 8 (80%) PCR positive patients with surgical appendix had the average number of obtained parasites that was 10.63 which was significantly higher than the group without appendectomy (P≤0.05); that is appendectomy was associated with infection in immunosuppressive cases. Conclusions: The pregnant women with immunocompromised condition are at a risk for toxoplasmosis and finally abortion; all T. gondii positive patients should be followed up with real-time PCR techniques