A recently described quantitative rapid cycle real time PCR (LightCycler™) assay detects Cryptosporidium parvum after in vitro excystation, which is a surrogate marker for the viability of the organisms. In the original assay the quantification standard is a dilution series of C. parvum oocysts with a microscopically determined excystation rate. The need to keep suspensions of viable oocysts in stock and to continuously monitor their excystation rate, however, renders the assay impracticable for routine application. A synthetic standard was developed to replace the in vivo standard and was calibrated using oocysts with known excystation rates. The standard consists of a 486 bp DNA segment ranging from 229 bp upstream to 79 bp downstream of the actual PCR target site. Aliquots of the standard were frozen and stored at −20 °C and at −70 °C or lyophilised and stored at room temperature in the dark. For a period of one year samples preserved with each of the three methods were restored every four or five weeks. They were amplified in the LightCycler™ and the crossing points (CP) were monitored. No significant trend in the raw CP values could be observed for any of the three storage methods. However, when the methods were compared to each other by calculating the CP ratios (−20 °C/−70 °C; −20 °C/lyophilised; −70 °C/lyophilised) at the 10 monitoring dates, the CP ratios −20 °C/−70 °C and −20 °C/lyophilised showed a highly significant positive trend (p<0.0001) while the CP ratio −70 °C/lyophilised did not differ from the null hypothesis (p=0.53). It can be concluded that the latter two preservation methods are both appropriate, while storage at −20 °C is less advisable. Calculations based on the molecular weight of the standard and on the assumption of an average yield of three sporozoites per oocyst led to the conclusion that the target sequence is probably located on a double copy gene