We developed rapid detection methods for pathogenic organisms based on immunomagnetic separation and flow cytometry (IMS-FCM). Benefits of these methods are the short time to result of around 80-120 minutes and results of similar or better quality compared to conventional methods. The target organisms selected for this work were the protozoan parasites Giardia lamblia and Cryptosporidium parvum and the bacterium Legionelle pneumophila (Lp). G. lamblia and C. parvum are important waterborne pathogens that are among the most common intestinal parasites of humans worldwide. Reliable, sensitive, quantitative, and mobile rapid screening methods for pathogenic organisms are not readily available yet, but would provide a great benefit to routine drinking water analysis but also to humanitarian intervention units in disaster situations. Conventional detection relies on (oo)cyst concentration, isolation, and confirmation with immunofluorescent microscopy (IFM), resulting in low recoveries and high detection limits. Many different immunomagnetic separation (IMS) procedures have been developed for separation and cyst purification, so far, with variable but high losses of cysts. Here, a method was developed for Giardia lamblia and Cryptosporidium parvum detection that requires less than 100 minutes and consists of filtration, resuspension, IMS and flow cytometric (FCM) detection. For Giardia spiked samples, recoveries exceeding 90% were obtained and false-positive results were never encountered in negative samples. Depending on how many liters of water are analyzed, the detection limit ranges from 0.1 to 40 cysts per liter. [...]