Molecular typing of several cheeses was achieved by PCR-DGGE analysis of microbial DNA directly extracted from the dairy samples. Cheese-specific fingerprints were obtained analyzing the variable V3 region of 16S rDNA, the profiles showed to be repeatable and reliable after repeated analysis of the same sample. Statistical analysis of molecular data showed relevant differences among cheeses highlighting the potential of the PCR-DGGE fingerprinting for the discrimination of dairy products. The variability of the fingerprints obtained by different samples of the same type of cheese definitely compromises the use of the technique to develop class-specific profiles to be used for cheeses classification, allowing just to detect the degree of complexity of the microbiota.