The aim of this work was to analyse a group of 69 lactobacilli isolated from dental caries and root canals of the extracted teeth from early childhood caries (ECC) affected children up to age of six. Clinical samples obtained from individual patients were cultivated in a 5 % CO2 atmosphere on MRS agar and/or BHI agar supplemented by 10 % sheep blood. Biochemical and physiological properties of all strains were characterized by API 50CH kit and conventional tube tests. Rep-PCR fingerprinting with the (GTG)5 primer was used for genotype characterization and identification of the isolates. Evaluation of obtained (GTG)5-PCR fingerprints assigned clearly 21 strains as Lactobacillus rhamnosus, 20 as Lactobacillus fermentum, 16 as Lactobacillus casei/paracasei, 7 as Lactobacillus salivarius, 4 as Lactobacillus plantarum and 1 as Lactobacillus gasseri.