Encephalitozoon cuniculi (E. cuniculi) is a fungus that behaves as an intracellular parasite infecting different types of cells. In rabbits and immunosuppressed animals of other species, including humans, it parasites neural tissues causing a highly characteristic neurological syndrome, for which repertory analysis indicates Phosphorus. Successful treatment of 7 naturally infected rabbits with Phosphorus confirmed that this medicine probably is the remedy of the ‘epidemic genius’ of microsporidiosis. In the present study, an in vitro model was used to evidence the intracellular relationship between macrophages and E. cuniculi after treatment of co-cultures with different potencies of Phosphorus. RAW 254.7 macrophages were co-cultivated with E. cuniculi and treated with Phosphorus 6cH, 30cH and 200cH. Controls were untreated co-cultures and cultures treated with vehicle (0.06% final alcohol concentration). Phagocytosis and lysosome activity were after after 1 and 24 hours of incubation by means of the calcofluor and acridine orange staining methods, followed by automatic image analysis (Metamorph®). Cytokine production was assessed with the MAGPIX®-Luminex system. The vehicle increased IL-6, MCP-1 and MIP1 production (p