The interaction of multi-walled carbon nanotubes (MWNTs) with living unicellular protozoan Stylonychia mytilus was studied. The results indicated that MWNTs were ingested largely by Stylonychia mytilus. Distribution of MWNTs in the cells, redistribution during dividing process of the cells, and excretion from the cells were observed successfully with optical microscope. The dependence of viability of Stylonychia mytilus was determined on the concentration of MWNTs, ranging from 0.1 microg/ml to 200 microg/ml. It was found that exposure of Stylonychia mytilus to the MWNTs with concentration higher than 1.0 microg/ml induced a dose-dependent growth inhibition to the cells and the damage occurred, by fluorescence microscopy, on the macronucleus and external membrane of the cells. The ultrastructure change by electron microscope revealed that the MWNTs exclusively localized to the mitochondria of the cells. It was proposed that the damage of macronucleus, micronucleus, and membrane of the cells, as well as growth inhibition of the cells might be a result of the damage of mitochondria, following this exclusive localization. Our finding provides important information on the bio-security of MWNTs and their migration in aqueous environment.