It has been apparent for some time that cyst numbers in the brain can be controlled endogenously yet identification of the exact effector mechanisms has not been so apparent. In these studies we demonstrate the presence of a distinct population of macrophages in the brain during chronic Toxoplasma infection, which express CXCR3, MMR, stabilin-1 and arginase-1. Furthermore these macrophages have chitinase activity, are localized to cysts and are observed in association with cyst degradation. The mechanism of cyst lysis is dependent on AMCase and this enzyme is required for survival during chronic infection to reduce parasite burden. The continuous presence of Toxoplasmic cysts in the brain and other tissues presents a constant threat of reactivation to the immune compromised patient. Mechanisms that enhance cyst removal or prevent their reactivation during Toxoplasma or other protozoan infections would provide a novel line of anti-parasitic therapies.