The aim of the present study was to determine the prevalence of Toxoplasma gondii antibodies in serum samples from two groups of women in Sudan and to use molecular techniques for detection of the organism’s DNA using B1 gene. The first group (study group) composed of 94 individuals and they aborted during the study, while the second group (control group) also composed of 94 individuals who gave birth to healthy children without complications. Serological screening using enzyme linked immunosorbent assay (ELISA) kits resulted in 39.4% and 35.1% of the women in the control and study group showed positive IgG antibodies to T. gondii respectively. PCR amplification of B1 gene resulted in detection of PCR product in 19.1% of the study group and 22.3% of the control group. There was no association between positive toxoplasmosis antibodies and abortion, furthermore, the individuals with positive PCR results in the control group did not abort. The usefulness of the B1 gene as a target for toxoplasmosis diagnosis was documented and the possible source of infection in the control and the study groups was discussed.