Seven patients with childhood-type hypophosphatasia and healthy control subjects were analysed for microbiological and clinical evidence of periodontitis. The bacterial composition of the subgingival plaque was analysed by 16S rRNA gene cloning and sequencing, DNA-DNA hybridisation with specific probes, and specific PCR. With the exception of the genus Veillonella and the species Eikenella corrodens, no differences between the cohorts in the composition of bacterial orders, families, genera, and species were observed. Accordingly, patients showed only slightly more bleeding on probing (BOP), and slightly higher periodontal probing depth (PPD) values than controls. Although this pilot study did not have the power to assess the prevalence of periodontitis in HP, we suggest that most paediatric patients suffering from HP harbour a subgingival microbiota, which is comparable to that of the healthy population.