Cell numbers of presumptive lactic acid bacteria varied markedly between 7 natural whey starter cultures (NWSC) used for producing traditional cows' milk Mozzarella cheeses in the Apulia region of Southern Italy. Taxonomic identification revealed a large diversity at species level, including mesophilic and thermophilic lactobacilli, lactococci, streptococci and enterococci. Randomly Amplified Polymorphic DNA (RAPD-PCR), analysis showed the biodiversity among the strains and, for lactobacilli, some relationships with provenience of the natural starter. Cell numbers of presumptive lactic acid bacteria in the corresponding Mozzarella cheeses were similar or higher than those found in the corresponding NWSC. RAPD-PCR analyses showed that most of the strains in cheese originated from the starter. The gross composition varied markedly between the 7 Mozzarella cheeses and ranged from 53-64% moisture, 17-23% protein, 13-20% fat and 0.50-1.61% salt. The values of pH for several samples were above 6.0. As shown by urea-PAGE of the pH 4.6-insoluble nitrogen fractions, cheese samples were characterized by differences in αs1- and p-casein hydrolysis. Cheeses also differed with respect to secondary proteolysis as shown by Principal Component Analysis (PCA) of data from RP-HPLC of the pH 4.6-soluble, pH 4.6-70% ethanol-soluble and 70% ethanol-insoluble nitrogen fractions. These differences were attributed to the different microbial composition of the NWSC. Strain selection and optimization of a protocol for producing a natural whey starter culture to be used by dairy factories of the Apulia region appears to be a pre-requisite to standardize the major traits distinguishing this cheese variety.