In this research characterization of the autochthonous lactic acid bacteria (LAB) population, naturally present in traditional Croatian products, fresh cheese and sauerkraut, was carried out, aimed to define potential probiotic starter cultures. Microbiological analysis revealed that LAB represent dominant autochthonous population in these high quality products and this was confirmed by the PCR-DGGE. After the autochthonous bacterial isolates were characterized as gram-positive, catalase-negative, asporogenous either cocci or rods that synthesize high concentration of lactic acid, by classical microbiological methods, further phenotypic characterization by SDS-PAGE electrophoresis of the whole cell proteins and by API 50 CHL test was performed. As a high level of probiotic survival in the gastrointestinal tract (GIT) is one of the most important criteria in probiotic selection, all eligible autochthonous strains were examined for their ability to survive harsh simulated GIT conditions. 2 different bacterial strains were selected from the autochthonous fresh cheeses and 5 from spontaneously fermented sauerkraut, which were discriminated as a different LAB strains by the RAPD analysis of DNA profiles obtained with specific oligonucleotides. Autochthonous isolates A7 and A8 but also SF1, SF2, SF4, SF9, SF13 showed high survival rates in the GIT in vitro. Selected isolates were susceptible to the tested antibiotics excluding vancomycin, for which representatives of the Lactobacillus species have an innate resistance. All selected strains fulfilled important selection criteria for probiotics: antimicrobial activity, autoaggregation ability, coaggregation with potential food pathogens, and adhesion to Caco-2 cell line. Finally, dry active preparation of the selected bacterial strains was obtained by freeze-drying. Viable cell count of the freeze-dried cultures was maintained high as it was cca 1010 CFU/g, what is of importance from the technological aspect due to the preparation, storage and application of the probiotic strains.