Experimental activation of peritoneal macrophages by interferon gamma (IFN-γ) resulted in the inhibition of Encephalitozoon cuniculi replication. However, E. cuniculi could replicate either in a non-activated cell line of murine macrophages PMJ2-R or in IFN-γ-activated PMJ2-R cells. Moreover, activation with IFN-γ led to faster replication of E. cuniculi in these cells. Opsonisation of E. cuniculi spores with anti-E. cuniculi polyclonal antibody did not affect E. cuniculi replication in both, non-activated and activated murine macrophages. In contrast, opsonisation of E. cuniculi spores caused the most effective replication of E. cuniculi in activated PMJ2-R cells. However, production of nitric oxide by these cells was significantly more intensive than that in non-activated, infected cells, where the parasite replicated to a much lesser extent. Our results support the hypothesis that E. cuniculi uses phagocytosis for the infection of host cells. They also indicate that the mechanism by which spores of E. cuniculi are killed by macrophages is not dependent on nitric oxide and they reveal that PMJ2-R cells cannot substitute peritoneal murine macrophages in immunological studies on E. cuniculi.