Periodontitis is a multi-microbial disease and the comparison of a series of periodontopathogenic and non-periodontopathogenic bacteria in terms of microbe-host interaction may provide clues to understand the microbial etiology of the disease better. When we deal with twenty different bacterial species in a study, the first technical issue is how to measure the accurate concentration and use the same number of bacterial cells. We measured bacterial concentration by enumerating bacteria stained with SYTOX green for constant time using a flow cytometer and compared the results with those obtained by plate counting. Concentrations calculated by two different methods were very close. Therefore, flow cytometric counting allowed the rapid analysis of live/dead bacteria, offering the advantage of turbidity measurement and that of colony counting together.