Aim: This was to characterise the microbial diversity in the complex dental plaque of children with severe early-childhood caries (S-ECC), using the denaturing gel gradient electrophoresis (DGGE) technique. Methods: The DGGE technique was used as a diagnostic tool to analyse samples from the oral cavity of a patient with S-ECC. Dental plaque samples from a 3-year-old child with S-ECC were taken from the primary central maxillary incisor (biofilm on vestibular surface), primary maxillary molar (biofilm on vestibular surface), primary central maxillary incisor (dentine), primary maxillary molar (dentine) and saliva and then analysed by PCR-DGGE. Results: Three bands occurred in all samples, moreover, 86% of similarity was observed in the pattern of bands between incisor and molar teeth biofilm samples, including four similar bands. Conclusion: DGGE is a valuable tool for differentiating the microbial composition of the oral plaque in S-ECC children.