A study was performed to evaluate the use of MS 2 phages and Bacillus subtilis spores as microbial indicators for Giardia and Cryptosporidium inactivation when disinfecting with chlorine dioxide. Microbial spiking experiments were performed at bench-scale in batch systems. Factors such as water matrix, temperature, contact time, chlorine dioxide dose and filtration stress (as simulated by a bench-scale sand shearing procedure) were examined to assess their impact on microbial inactivation. Results indicate that Bacillus subtilis spores may be a feasible microbial indicator for the inactivation of Cryptosporidium oocysts. Furthermore, shearing stress appears to promote microbial inactivation at 20?C. Consequently, published CxT values may have an additional safety factor included in them when this approach is applied to calculate microbial inactivation resulting from the addition of chlorine dioxide at a post-filter location.