Immunomagnetic separation (IMS) was employed for the isolation of Cryptosporidium oocysts from five different water matrices (n=3). Oocysts within the resultant supernatants were captured using membrane filtration and incubated with a fluorescent monoclonal antibody (FITC-mAb) and 4,6 diamidino-2-phenyl indole (DAPI). After this labeling procedure, a laser scanning instrument (ChemScan RDI) was used for the rapid detection and enumeration of labeled oocysts. The recovery efficiency of the IMS procedure was found to be high with a mean percentage recovery of 82.1% (range 78.5-86.3). This study demonstrates that IMS provides an efficient technique for the isolation of oocysts from water concentrates. In addition, laser scanning was found to be a reliable technique which was faster and easier to perform than the manual examination of sample preparations using epifluorescence microscopy. Includes 6 references, table.