Toxoplasmosis, caused by the obligate intracellular parasite Toxoplasma gondii, is one of the most prevalent zoonotic parasitic infections worldwide. When acquired during pregnancy, T. gondii can be transmitted to the fetus, with clinical outcomes influenced by gestational age at time of infection and the parasite’s genotype. Prenatal screening enables the detection of maternal seroconversion and offers a critical window for intervention. In Uruguay, despite mandatory serological screening during pregnancy, national data on T. gondii seroprevalence and maternal seroconversion have not been updated in two decades. In addition, the genetic diversity of local strains remains poorly characterized. In this study, we analysed publicly available serological data from pregnant individuals attending Uruguay’s largest public maternity hospital between 2019 and 2023. We found that seroprevalence has modestly declined from 50% (reported in 1998) to 45.5%, with a congenital transmission rate of 0.58%. Clinical analysis of affected newborns revealed chorioretinitis as the predominant manifestation. To investigate parasite diversity, we performed genotyping of T. gondii strains using in silico PCR-RFLP following molecular detection. Our findings revealed substantial genetic diversity, including novel allele combinations not previously described in the region. These results highlight both the continued public health burden and the evolving genetic landscape of T. gondii in Uruguay. Our findings underscore the need to strengthen surveillance and prevention strategies for congenital toxoplasmosis in South America.