We studied the cytotoxic effect of the heavy metals Cd, Zn and Cu on three different species of ciliated protozoa isolated from an urban wastewater treatment plant. The order of toxicity was Cd>Cu>>Zn or Cu>Cd>>Zn, depending on the microbial species. In bimetallic (Cd+Zn) treatments, results indicated that, in general, the presence of Zn in the same medium decreased Cd cytotoxicity. Both cellular assays and microscopic observations showed that bioaccumulation is an important mechanism of resistance to these toxic environmental pollutants in such eukaryotic microorganisms. However, bioaccumulation might not be the main mechanism involved in Cu resistance. For the first time, fluorescence methodology was applied for revealing metal deposits in the cellular cytoplasm. This microscopic method is only useful when cell cultures can be exposed to rather high metal concentrations, as in the case of Zn. Inside the ciliated protozoa exposed to sublethal concentrations of Cd or Zn, it is possible to observe diverse electron-dense granules by TEM which are not seen in controls. Problems in comparing our results on heavy metal cytotoxic effects on ciliates with already published data are exposed and discussed. The use of these eukaryotic microorganisms as potential whole cells or molecular (ciliate metallothioneins) biosensors seems to be a reasonable useful alternative for assessing metallic pollution.