Cytometric analysis allows for the quantitative and qualitative evaluation of microorganisms in food. Apparatus for food analysis is available on the market for use in the food processing industry and increasingly displaces traditional methods. Apart from being a full automated method, an important advantage of cytometric analysis is a multi-parametric assessment of the physiological state of bacterial cells. This paper presents examples of cytometric analysis applications in both solid-phase and flow systems in microbiological studies of food. The viable but nonculturable (VBNC) state of various microorganisms has been distinguished, which can be determined using the cytometric approach.