Many of the indigenous foods consumed around the world are produced by natural fermentation. Information is not always available about the microorganisms involved, which makes it very difficult to maintain the product quality. In this work the microflora of the traditional Bulgarian cereal-based beverage boza was investigated and some of the yeast and lactic acid bacteria strains have been identified and quantified. Although further work is needed to identify what microorganisms are responsible for the beneficial properties of Bulgarian boza these results could form the basis for the improvement of product quality and consistency, and could also be used to develop new cereal-based foods in Western Europe.