Aim: This study evaluated the oral status and microbiota of HIV+ youth infected by vertical transmission. Materials & methods: 34 HIV+ and 36 HIV- individuals (14–24 years of age) were examined for oral infections/lesions. Subgingival biofilm was collected and the microbiota determined by checkerboard DNA–DNA hybridization. Results: Over 90% of the HIV+ youth were under highly active antiretroviral therapy, but 64.6% had AIDS and 47% presented oral manifestations. HIV+ youth showed more periodontal attachment loss and inflammation than HIV- (p < 0.05), and also high prevalence of caries. Most species were detected in higher prevalence in the microbiota of HIV+ than controls. Conclusion: HIV+ youth infected by vertical transmission presented more periodontal destruction and inflammation, and greater prevalence of microbial pathogens compared with HIV- individuals.