To assess whether the probiotic food supplements, produced and distributed on the Italian market during 2005-2006, complied with the Italian Guidelines on Prebiotics and Probiotics, 72 samples from 29 processing plants were analyzed. The survey included 41 samples from processing plants and 31 samples of the same brand from retailers collected at timed intervals (3, 8 and 13 months). A polyphasic approach based on a suitable analytical collection method (genotypic identification of total bacteria - differential presumptive enumeration - genotypic identification of viable bacteria) was adopted to identify and quantify the microorganisms labelled and recovered from the probiotic supplements examined. Most supplements analyzed (87%) did not conform to the Italian guidelines and the differences were both quantitative and qualitative (number determination, purity, types and viability of microorganisms). Even though most labelled supplements (25 samples) indicated the presence of Bifidobacterium bifidum, this organism was only detected sporadically and always as dead cells. Unexpected results were obtained during our survey due to the absence of viability of Bacillus coagulans spores in some labelled supplements. Besides this, some of these supplements also contained other spore-forming species, identified as B. cereus that are toxin producing. We have also documented a widespread use of misclassified microbial species or species with fictitious names. The main factors involved in the absence of compliance were examined and the poor quality control applied by manufacturers was emphasized.