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Toxoplasmosis caused by the intracellular parasite Toxoplasma gondii, is characterized by a life-long chronic infection. The parasite is an efficient neurotropic infectious agent that establishes its “safe” life by forming intracellular cysts in chronically infected animals and humans. This protocol describes the specific recipes and method to stain brain cysts from infected mice and rats for further quantification using epifluorescence microscopy. This method provides the possibility to scan the entire brain and thus to numerate all cysts.