Objective The objective of this study was to evaluate the probiotic potential as well as the ability of adhesion and aggregation of natural and autochthonous lactic acid bacteria, isolated from traditionally made cheese. Results Lactic acid bacteria from natural food sources can be promising probiotic candidates and they can be used in natural food preservation or like starter cultures. Tested autochthonous isolates showed tolerance to the simulated gastrointestinal condition as well as the sensitivity to clinically relevant antibiotics, especially to ampicillin (MIC at 0.195 mu g mL(-1) for lactobacilli and from 0.195 to 3.125 mu g mL(-1) for lactococci). Among isolates, the highest percentage of adhesion was detected with chloroform, while the adhesion ability of selected isolates to pig intestinal epithelium was in the correlation with the results of adhesion ability with solvents. The auto-aggregation ability of isolates was demonstrated, while co-aggregation with Escherichia coli was strain specific. Conclusion The results indicated the potential probiotic properties of the isolates and give evidence for further investigation and potential application in the dairy industry.