Toxoplasma gondii is a parasitic protist that is the agent of toxoplasmosis. It is capable of infecting all mammals, including humans. The infection is mainly asymptomatic in immunocompetent patients, but in case of immunosuppression or for the congenital form of toxoplasmosis it can lead to severe pathologies with a possible fatal outcome. T. gondii contains two organelles of endosymbiotic origin: the mitochondrion and the apicoplast, which is a non-photosynthetic plastid. These organelles contain important biochemical pathways which might be interesting targets for future therapeutic strategies. Iron-sulfur clusters are one of the most ancient and ubiquitous prosthetic groups, and they are required by a variety of proteins involved in important metabolic processes. As for plants, T. gondii has several pathways for biosynthesis of iron-sulfur proteins, located in three different cellular compartments: the cytoplasm, the mitochondrion and the apicoplast. We have investigated the relative contributions of the mitochondrion and the apicoplast to the iron-sulfur proteome of the parasite by generating specific mutants for key proteins of the mitochondrial (TgIscU) and plastidic (TgSufS) pathways, on which we performed a quantitative proteomic analysis.