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The introduction of immunomagnetic separation (IMS) into water analysis for Cryptosporidium parvum oocysts was an important and significant improvement to previous methods. However, variation in IMS performance has been observed in some water matrices, and has previously been tentatively linked to pH and other matrix factors. Here we investigated different factors that might influence Cryptosporidium oocyst recovery during IMS, including pellet size, pH and IMS system. Our results indicate that with the Dynal IMS system, the buffering capacity of the buffers is insufficient to accommodate all water concentrates and manual adjustment of pH following addition of IMS buffers may improve recoveries up to between 20-30% in problematic samples. However a different IMS system (Aureon Biosystems) had buffers with superior pH buffering capabilities, which required no manipulation. Furthermore, the Aureon IMS system produced greater recovery efficiencies to the Dynal system, even when the pH of the Dynal system was manually adjusted. Additionally, the Aureon IMS system demonstrated higher oocyst recoveries in samples with larger packed pellet volumes more consistently than the Dynal IMS system. The IMS process is a central component for the efficient recovery of Cryptosporidium oocysts; these results suggest that the new IMS system should be considered as an alternative to the existing IMS systems. Includes 15 references, tables, figure.