The aim of this study was to demonstrate that flow cytometry (FACS) could potentially be employed for rapid viability assessment of probiotic bacteria immobilized or encapsulated in complex matrices. Lactobacillus rhamnosus GG was immobilized within six different protein environments using whey protein isolate (WPI) and yoghurt matrices and encapsulated within protein micro-beads, all of which ranged in structural complexity. Following a series of environmental-stress trials, survival of the strain was examined using FACS compared to traditional plate count techniques. Cell extraction and digestive pre-treatments were designed to release cells and reduce the protein background, respectively, which represent compositional obstacles for efficient FACS analysis. Physico-chemical properties of protein-probiotic components revealed the mechanism necessary for efficient cell delivery during FACS analysis. This assay required 40 min sample preparation and distinct functional populations were discriminated based on fluorescent properties of thiazole orange (TO) and propidium iodide (PI). This assay yielded 45-50 samples/h, a detection range of 10(2)-10(10) cfu/ml of homogenate and generated correlation coefficients (r) of 0.95, 0.92 and 0.93 in relation to standard plate counts during heat, acid and storage trials, respectively. In conclusion, this methodology provides impetus for dynamic progression of FACS for rapid viability assessment of live bacteria immobilized/encapsulated within complex protein systems. (C) 2010 Elsevier B.V. All rights reserved.