Generalized pre-pubertal periodontitis (GPP) is a rare entity that usually affects children with severe systemic diseases. We report the case of a 7-year-old male patient diagnosed with GPP, with no apparent systemic condition, who lost all his primary teeth to periodontal disease. Before extractions, while he was still in mixed dentition the subgingival plaque was collected and analyzed using DNA probes to 40 different microorganisms. Putative periodontopathogens such as Prevotella intermedia, Selenomonas noxia, Fusobacterium nucleatum, and Actinobacillus actinomycetemcomitans could be identified throughout the mouth. More intriguing was the colonization of the sulcus of some secondary teeth by potentially harmful microorganisms found in pockets of diseased adjacent primary teeth.