We measured ingestion and digestion rates of the pathogenic bacterium Campylobacter jejuni by a freshwater ciliate Colpoda sp. to determine whether Campylobacter is able to resist protist digestion. Campylobacter and the nonpathogenic bacterium Pseudomonas putida LH1 were labeled with a 5-chloromethylfluorescein diacetate, which fluoresces in intact and active cells but fades when exposed to low pH environments, such as protistan food vacuoles. Ingestion and digestion rates were measured via flow cytometry as the change in ciliate fluorescence over time, which corresponded to the quantity of intracellular bacteria. The rate of Campylobacter ingestion exceeded the digestion rate. Ciliates retained labeled Campylobacter 5 h after ingestion was stopped. In contrast, ciliates grazing upon P. putida returned to baseline fluorescence within 5 h, indicating that P. putida were completely digested. The ability of intracellular Campylobacter to remain viable after ingestion was tested by sorting individual ciliates and bacterial cells into Campylobacter-selective media. Campylobacter growth occurred in 15% (± 5 SE) of wells seeded with highly fluorescent ciliates, whereas only 4% (± 1) of wells seeded with free-living Campylobacter exhibited growth. A key advantage of this approach is that it is rapid and should be applicable to other phagocytotis studies.