BACKGROUND Toxoplasmosis is a zoonotic disease that affects a wide range of animals, including small ruminants. Sheep and goats are considered as biological indicators for the contamination of the environment with Toxoplasma gondii oocysts. In addition, in countries such as Egypt, where sheep and goat meat is frequently consumed, T. gondii infection in small ruminants may also pose a public health risk. To establish baseline estimates of the prevalence of T. gondii infection in Egyptian small ruminants, we used an indirect immunofluorescence assay (IFA) and an enzyme-linked immunosorbent assay (ELISA) to assess the seroprevalence in 398 sheep from four Egyptian governorates (Cairo, Giza, Dakahlia and Sharkia) and in 100 goats from Dakahlia. The positive and negative agreements of both tests were calculated and the true prevalence was estimated using a Bayesian approach. RESULTS The true prevalence of antibodies to T. gondii as determined by both tests was higher in Egyptian goats (62%) than in sheep for each province (between 4.1 and 26%). Sheep slaughtered at the Cairo abattoir had the lowest true prevalence (4.1%), while true prevalences in Dakahlia, Giza and Sharkia governorates (26%, 23% and 12%, respectively) were substantially higher. CONCLUSIONS The high prevalence of antibodies to T. gondii may indicate an important role of goat and sheep in the transmission of human toxoplasmosis in Egypt, given the habit of eating undercooked grilled mutton.