The immunity system status of an individual plays the key role in regulation of opportune infection. In the fight against the intracellular parasites several non-specific as well as specific immunity mechanisms are applied. The dominant role in response to infection caused by the representatives of genus Encephalitozoon plays the cell-mediated immune response. Encephalitozoon cuniculi, as the most explored representative of this genus is able to survive in the host organism despite his active immunity response. Latent asymptomatic infection goes on only as long as the parasite multiplication and immune response are balanced.