Our research on the mechanisms of action of chlorine-based oxidants on Cryptosporidium parvum oocysts in water revealed a dual-phase effect: (i) response to oxidative stress, which was demonstrated by induced expression of the Hsp70 heat shock gene, and (ii) oocyst inactivation as a result of long-term exposure to oxidants. The relative biocidal effects of sodium hypochlorite (bleach) and electrolytically generated mixed oxidant solution (MOS) on C. parvum oocysts were compared at identical free chlorine concentrations. Oocyst inactivation was determined by quantitative reverse transcription-PCR (qRT-PCR) amplification of the heatinduced Hsp70 mRNA and compared with tissue culture infectivity. According to both assays, within the range between 25 and 250 mg/liter free chlorine and with 4 h contact time, MOS exhibits a higher efficacy in oocyst inactivation than hypochlorite. Other RNA-based viability assays, aimed at monitoring the levels of -tubulin mRNA and 18S rRNA, showed relatively slow decay rates of these molecules following disinfection by chlorinebased oxidants, rendering these molecular diagnostic viability markers inappropriate for disinfection efficacy assessment.Cryptosporidia, the etiological agents of cryptosporidiosis outbreaks worldwide, are known for their remarkable ability to withstand chlorination even at free chlorine levels far exceeding those normally employed in water treatment processes (3,7,17,19).Research on protozoan oocyst inactivation by chemical disinfectants has been somewhat hindered by the lack of reliable and rapid quantitative assay methods for assessing inactivation and viability in Cryptosporidium oocyst populations (4). Undoubtedly, oocyst infectivity is the best way to measure disinfection efficacy (12, 25), but this technique requires specialized laboratory setup and has a relatively long turnaround time.The initial goal of this study was to evaluate the applicability of different molecular markers for the development of a rapid and potentially field-deployable quantitative PCR (qPCR) assay for assessing oocyst viability directly, without an intermediate cell culture or animal infection step, as well as to demonstrate the applicability of such a rapid assay for evaluating the biocidal efficacy of chlorine-based oxidants and of other disinfection techniques. As such, in the water treatment practice, a qPCR-based assay could be applied (i) when immediate decisions are needed to respond to a detectable water threat and mitigate the potential health consequences, (ii) for rapid assessment of disinfection efficacy when it needs to be quantified within the time frame of a few hours following chemical or UV disinfection, and (iii) to rapidly adjust and optimize disinfection dose rates to reduce the use of disinfection chemicals when possible and therefore reduce disinfection by-product formation in the finished water. At the same time, the qPCR assay may provide a valuable research tool for better understanding the molecular and cellular nature of the chlorine resistance of pr...