Background Globally, congenital toxoplasmosis remains a significant cause of morbidity and mortality, and outbreaks of T. gondii infection represent a major public health threat, especially in developing countries. Evidence in the literature indicates that only a few studies have been conducted on the incidence of maternal and congenital toxoplasmosis in Saudi Arabia. This prospective study aims to measure the overall incidence of congenital toxoplasmosis, both patent and ‘silent’ infection, among pregnant women in the Eastern Province of Saudi Arabia. The study would attempt to relate the cord blood results with the time of seroconversion in the mother, underlining the importance of early intervention in such cases. Methods Five hundred paired maternal/cord blood samples were tested for anti-Toxoplasma IgG or IgM antibodies. Samples were collected during delivery from mother and newborn (cord blood) from November 2011 to May 2012. Only positive for anti-Toxoplasma IgG or/and IgM cord blood was processed for real-time PCR for confirmation. The age of mothers ranged from 16 to 45 years. Results The sample subjects were tested during child delivery for specific IgG and IgM antibodies against Toxoplasmosis, of which 21.0% (n = 105) mother/baby pairs were found serologically positive for anti-Toxoplasma IgG antibodies. The rate of maternal seropositivity for anti-Toxoplasma IgM antibodies was found among 4 participants (0.8%), who were also seropositive for anti-Toxoplasma IgG antibodies. None of the children tested positive for anti-Toxoplasma IgM antibodies, even those born to mothers with IgM positive. All 105 cord blood tests in the study sample were confirmed negative by real-time PCR. The seroprevalence of Toxoplasma IgG antibodies increased with maternal age, parity, and was significantly higher in women who gave birth to children with congenital anomalies (p = 0.008). Conclusion The findings of the current study indicate a dire need to develop and implement preventive programs against Toxoplasma gondii infection, as well as a health education program on how to avoid toxoplasmosis for all seronegative women during pregnancy.